Journal of Microbiology

Journal Article

Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection: Xiaomin Lin, Chun Lin, Xin Li, Fen Yao, Xiaoling Guo, Meimei Wang, Mi Zeng, Yumeng Yuan, Qingdong Xie, Xudong Huang, Xiaoyang Jiao; J. Microbiol. 2024;62(12):1113-1124. Published online December 2, 2024; DOI: https://doi.org/10.1007/s12275-024-00190-5

319 View
7 Download
1 Web of Science
1 Crossref

To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.

Citations

Citations to this article as recorded by

Targeting gut microbiotasu-derived butyrate for Ferroptosis inhibition in Sepsis-induced myocardial dysfunction
Jianfei Xiong, Guoxiang Liu, Tianyuan Jia, Qian Yang, Changqing Zhu, Shiwei Wang
Journal of Molecular and Cellular Cardiology.2025;[Epub] CrossRef

Review

The Role of Extracellular Vesicles in Pandemic Viral Infections: Woosung Shim, Anjae Lee, Jung-Hyun Lee; J. Microbiol. 2024;62(6):419-427. Published online June 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00144-x

418 View
5 Download
2 Web of Science
1 Crossref

Abstract PDF

Extracellular vesicles (EVs), of diverse origin and content, are membranous structures secreted by a broad range of cell types. Recent advances in molecular biology have highlighted the pivotal role of EVs in mediating intercellular communication, facilitated by their ability to transport a diverse range of biomolecules, including proteins, lipids, DNA, RNA and metabolites. A striking feature of EVs is their ability to exert dual effects during viral infections, involving both proviral and antiviral effects. This review explores the dual roles of EVs, particularly in the context of pandemic viruses such as HIV-1 and SARS-CoV-2. On the one hand, EVs can enhance viral replication and exacerbate pathogenesis by transferring viral components to susceptible cells. On the other hand, they have intrinsic antiviral properties, including activation of immune responses and direct inhibition of viral infection. By exploring these contrasting functions, our review emphasizes the complexity of EV-mediated interactions in viral pathogenesis and highlights their potential as targets for therapeutic intervention. The insights obtained from investigating EVs in the context of HIV-1 and SARS-CoV-2 provide a deeper understanding of viral mechanisms and pathologies, and offer a new perspective on managing and mitigating the impact of these global health challenges.

Citations

Citations to this article as recorded by

Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
Tae-Hun Kim, Sojung Bae, Jinjong Myoung
Journal of Microbiology and Biotechnology.2024; 34(12): 2506. CrossRef

Journal Articles

The β‑Lactamase Activity at the Community Level Confers β‑Lactam Resistance to Bloom‑Forming Microcystis aeruginosa Ce: Yerim Park , Wonjae Kim , Minkyung Kim , Woojun Park; J. Microbiol. 2023;61(9):807-820. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00082-0

366 View
0 Download
9 Web of Science
7 Crossref

Abstract PDF

Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXArelated antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.

Citations

Citations to this article as recorded by

Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts
Wonjae Kim, Yerim Park, Minkyung Kim, Yeji Cha, Jaejoon Jung, Che Ok Jeon, Woojun Park
Ecotoxicology and Environmental Safety.2024; 277: 116375. CrossRef
Microcystis abundance is predictable through ambient bacterial communities: A data-oriented approach
Mingyeong Kang, Dong-Kyun Kim, Ve Van Le, So-Ra Ko, Jay Jung Lee, In-Chan Choi, Yuna Shin, Kyunghyun Kim, Chi-Yong Ahn
Journal of Environmental Management.2024; 368: 122128. CrossRef
Enhanced mechanical properties of living and regenerative building materials by filamentous Leptolyngbya boryana
Yongjun Son, Jihyeon Min, Indong Jang, Jiyoon Park, Chongku Yi, Woojun Park
Cell Reports Physical Science.2024; 5(8): 102098. CrossRef
Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms
Aabir Banerji, Nichole E. Brinkman, Benjamin Davis, Alison Franklin, Michael Jahne, Scott P. Keely
Microorganisms.2024; 12(11): 2121. CrossRef
Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
Journal of Microbiology.2024; 62(11): 933. CrossRef
Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park
Journal of Microbiology.2024; 62(3): 249. CrossRef
Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park
Harmful Algae.2024; 137: 102680. CrossRef

Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea: Miryung Kim , Yong Seok Kim , Chang Jun Cha; J. Microbiol. 2023;61(1):37-47. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-022-00008-2

413 View
0 Download
2 Web of Science
4 Crossref

Abstract PDF

Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rodshaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 ( C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).

Citations

Citations to this article as recorded by

Pilin regions that select for the small RNA phages in Pseudomonas aeruginosa type IV pilus
Hee-Won Bae, Hyeong-Jun Ki, Shin-Yae Choi, You-Hee Cho, Kristin N. Parent
Journal of Virology.2025;[Epub] CrossRef
Genomic insights into multidrug and heavy metal resistance in Chryseobacterium sp. BI5 isolated from sewage sludge
Mrinmoy Patra, Anand Kumar Pandey, Suresh Kumar Dubey
Total Environment Microbiology.2025; 1(1): 100005. CrossRef
Chryseobacterium cupriresistens sp. nov., a copper-resistant bacterium isolated from soil contaminated with heavy metals in Chapala Basin, Mexico
Ivan Arroyo-Herrera, Ana Laura Reséndiz-Martínez, Brenda Román-Ponce, Joseph Guevara-Luna, Xiaoxia Zhang, Ayixon Sánchez-Reyes, Paulina Estrada-de los Santos, En Tao Wang, María Soledad Vásquez-Murrieta
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Diversity and Dynamics of Marine Arenicolous Fungi in Three Seasides of the Korean Peninsula: Jun Won Lee , Chang Wan Seo , Wonjun Lee , Ji Seon Kim , Ki Hyeong Park , Yoonhee Cho , Young Woon Lim; J. Microbiol. 2023;61(1):63-82. Published online January 30, 2023; DOI: https://doi.org/10.1007/s12275-023-00011-1

365 View
1 Download
6 Web of Science
7 Crossref

Abstract PDF

Various arenicolous fungal species have been detected from the beach sand in the coastal area. However, little has been revealed regarding their distribution and dynamics. To investigate the overall diversity of marine arenicolous fungi (MAFs) in Korea and whether the composition of MAFs is affected by ocean currents, we isolated and analyzed the fungal community from the western, southern, and eastern seasides of the Korean Peninsula. In total, 603 strains were isolated and identified as 259 species based on appropriate molecular markers for each genus (ITS, BenA, CaM, tef1, and act). The composition of MAFs showed differences among the seasides. Our results indicate that many MAFs inhabit the beach sand on the Korean Peninsula, and the composition of MAFs is also affected by ocean currents flowing along each coast.

Citations

Citations to this article as recorded by

Inside out: New root endophytic Penicillium and Talaromyces species isolated from Cattleya orchids (Orchidaceae) in Brazil
T.O. Condé, D.O. Ramos, P.T.S. Nogueira, O.L. Pereira
Fungal Systematics and Evolution.2025; 15(1): 179. CrossRef
Taxonomic Study of Sixteen Unrecorded and Five New Species of Hypocreales from the Korean Marine Environment
Wonjun Lee, Ji Seon Kim, Sumin Jo, Chang Wan Seo, Young Woon Lim
Mycobiology.2025; 53(2): 144. CrossRef
Fungal frontiers in toxic terrain: Revealing culturable fungal communities in Serpentine paddy fields of Taiwan
Kai-Wen Cheng, Jiue-in Yang, Piroonporn Srimongkol, Marc Stadler, Aphichart Karnchanatat, Hiran A. Ariyawansa
IMA Fungus.2025;[Epub] CrossRef
Taxonomy, phylogeny, and bioactive potential of Xylariales (Sordariomycetes, Ascomycota) from Thailand: novel species discovery, new host and geographical records, and antibacterial properties
Achala R. Rathnayaka, K. W. Thilini Chethana, Areerat Manowong, Amuhenage T. Bhagya, Hsan Win, Zaw L. Tun, Ausana Mapook, Kevin D. Hyde
MycoKeys.2025; 120: 35. CrossRef
The genus Peniophora (Russulales, Basidiomycota) from Patagonia revisited
Mario Rajchenberg, Andrés de Errasti, Sergio Pérez Gorjón
Mycological Progress.2024;[Epub] CrossRef
Contributions to the Inocybe umbratica–paludinella (Agaricales) Group in China: Taxonomy, Species Diversity, and Molecular Phylogeny
Xin Chen, Wen-Jie Yu, Tolgor Bau, P. Brandon Matheny, Egon Horak, Yu Liu, Li-Wu Qin, Li-Ping Tang, Yu-Peng Ge, Tie-Zhi Liu, Yu-Guang Fan
Journal of Fungi.2024; 10(12): 893. CrossRef
Long-Term Investigation of Marine-Derived Aspergillus Diversity in the Republic of Korea
Jun Won Lee, Wonjun Lee, Rekhani Hansika Perera, Young Woon Lim
Mycobiology.2023; 51(6): 436. CrossRef

Flaviflexus equikiangi sp. nov. isolated from faeces of Equus kiang (Tibetan wild ass) and carrying a class 1 integron gene cassette in its genome: Caixin Yang , Xingxing Lian , Yanpeng Cheng , Yifan Jiao , Jing Yang , Kui Dong , Shan Lu , Xin-He Lai , Dong Jin , Han Zheng , Ji Pu , Suping Wang , Liyun Liu , Jianguo Xu; J. Microbiol. 2022;60(6):585-593. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1673-3

227 View
0 Download

Abstract PDF: Two Gram-stain-positive, catalase-negative, non-spore-forming, cocci-shaped strains (dk850T and JY899) were isolated from the feces of Equus kiang in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based phylogenetic analyses showed that strains dk850T and JY899 belong to the genus Flaviflexus, closest to F. salsibiostraticola KCTC 33148T, F. ciconiae KCTC 49253T and F. huanghaiensis H5T. The DNA G + C content of strain dk850T was 62.9%. The digital DNADNA hybridization values of strain dk850T with the closely related species were below the 70% threshold for species demarcation. The two strains grew best at 28°C on brain heart infusion (BHI) agar with 5% sheep blood. All strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-9(H4) was the major menaquinone in strain dk850T. The major polar lipids included diphosphatidylglycerol and an unidentified phospholipid. Strains dk850T and JY899 were identified as carrying a class 1 integron containing the aminoglycoside resistance gene aadA11, both strains were resistant to spectinomycin and streptomycin. Based on several lines of evidence from phenotypic and phylogenetic analyses, strains dk850T and JY899 represent a novel species of the genus Flaviflexus, for which the name Flaviflexus equikiangi sp. nov. is proposed. The type strain is dk850T (= CGMCC 1.16593T = JCM 33598T).

Randomized Controlled Trial

A split face study on the effect of an anti-acne product containing fermentation products of Enterococcus faecalis CBT SL-5 on skin microbiome modification and acne improvement: Hye Sung Han , Sun Hye Shin , Bo-Yun Choi , Nayeon Koo , Sanghyun Lim , Dooheon Son , Myung Jun Chung , Kui Young Park , Woo Jun Sul; J. Microbiol. 2022;60(5):488-495. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1520-6

590 View
0 Download
11 Web of Science
10 Crossref

Abstract PDF

Antibiotic-resistant Cutibacterium acnes and dysbiosis of the skin microbiome are of increasing concern in acne treatment. Enterococcus faecalis, a widely used probiotic, has shown benefits for acne treatment by exerting antimicrobial activity against C. acnes. Therefore, this study aimed to investigate the efficacy and safety of an E. faecalis CBT SL-5-extract-containing lotion in patients with mild-to-moderate acne. Twenty patients were enrolled in this randomized, placebo-controlled, split-face comparative study. Patients were treated with E. faecalis lotion on one side of the face and a vehicle lotion on the other side for 4 weeks. The efficacy outcome measures included improvement in the investigators’ assessment of acne severity, patient satisfaction, changes in skin parameters and diversity of the skin microbiome. The investigators’ assessment score was significantly improved on the test side compared to the control side, after 2 weeks (p = 0.009) and 6 weeks (p < 0.0005). However, TEWL and skin hydration were not significantly different between the two groups. The phylogenetic diversity of the skin microbiota decreased over time in the skin samples of test side. In conclusion, E. faecalis CBT SL-5 extract can be a feasible and well-tolerated option for improving acne severity and skin microbiome dysbiosis in mild-to-moderate acne patients.

Citations

Citations to this article as recorded by

Efficacy of a Postbiotic Formulation Combined With Microneedling for Mild‐to‐Moderate Acne: A Self‐Control Study
Zhanhong Li, Peihui Li, Yu Xu, Changqing Yan, Xiufen Ma, Huiying Wang, Hong Cheng, Jing Zeng, Ting Li, Xinxian Li, Jia Zhou, Jie Zhang, Jianfeng Zhou, Rongya Yang, Yan Wu, Li Li, Wei Lai, Jiangyun Zhao, Zhe Liu, Qiong Meng
Journal of Cosmetic Dermatology.2025;[Epub] CrossRef
Efficacy of Probiotic Supplements and Topical Applications in the Treatment of Acne: A Scoping Review of Current Results
Ida Ayu Manik Partha Sutema, Irma Latarissa, I Gusti Ayu Rai Widowati, Cynthia Retna Sartika, Ni Wayan Eka Ciptasari, Keri Lestari
Journal of Experimental Pharmacology.2025; Volume 17: 1. CrossRef
Acne vulgaris: advances in pathogenesis and prevention strategies
Weiping Xu, Jiahui Xu, Dandan Huang, Chen Wang, Jiajia Song, Xiaoyong Chen, Huayi Suo
European Journal of Clinical Microbiology & Infectious Diseases.2025; 44(3): 515. CrossRef
Analysis of global trends and hotspots of skin microbiome in acne: a bibliometric perspective
Lanfang Zhang, Yuan Cai, Lin Li, Jie Hu, Changsha Jia, Xu Kuang, Yi Zhou, Zhiai Lan, Chunyan Liu, Feng Jiang, Nana Sun, Ni Zeng
BioData Mining.2025;[Epub] CrossRef
Modulation of the microbiome: a paradigm shift in the treatment of acne
Tamara Searle, Firas Al-Niaimi, Faisal R Ali
Clinical and Experimental Dermatology.2025; 50(12): 2357. CrossRef
Integrated Metagenomic and Lipidomic Profiling Reveals Dysregulation of Facial Skin Microbiome in Moderate Acne Vulgaris
Xiaoye Qi, Zhaoying Han, Jie Meng, Hongrui Zhao, Maoyuan Zhou, Meichao Wang, Shengze Kang, Qingying Shi, Hongyan Li, Fuping Lu, Huabing Zhao
Microorganisms.2025; 13(12): 2674. CrossRef
Using probiotics to treat acne vulgaris: systematic review
Aleena Boby, Grace Lee, Nicole Natarelli, Lilia Correa
Archives of Dermatological Research.2024;[Epub] CrossRef
Skin Deep: The Potential of Microbiome Cosmetics
Ju Hee Han, Hei Sung Kim
Journal of Microbiology.2024; 62(3): 181. CrossRef
The updates and implications of cutaneous microbiota in acne
Cong Huang, Fan Zhuo, Baoquan Han, Wenting Li, Bin Jiang, Kaoyuan Zhang, Xingling Jian, Zhenzhen Chen, Hui Li, Haiyan Huang, Xia Dou, Bo Yu
Cell & Bioscience.2023;[Epub] CrossRef
Cutibacterium acnes Dysbiosis: Alternative Therapeutics for Clinical Application
Sara Sá, Ruben Fernandes, Álvaro Gestoso, José Mário Macedo, Daniela Martins-Mendes, Ana Cláudia Pereira, Pilar Baylina
Applied Sciences.2023; 13(21): 12086. CrossRef

Journal Article

Alterations of oral microbiota in Chinese children with viral encephalitis and/or viral meningitis: Yijie Li , Jing Liu , Yimin Zhu , Chunying Peng , Yao Dong , Lili Liu , Yining He , Guoping Lu , Yingjie Zheng; J. Microbiol. 2022;60(4):429-437. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1560-y

348 View
0 Download
3 Web of Science
3 Crossref

Abstract PDF

The role of oral microbiota in viral encephalitis and/or viral meningitis (VEVM) remains unclear. In this hospital-based, frequency-matched study, children with clinically diagnosed VEVM (n = 68) and those with other diseases (controls, n = 68) were recruited. Their oral swab samples were collected and the oral microbiota was profiled using 16S rRNA gene sequencing. The oral microbiota of children with VEVM exhibited different beta diversity metrics (unweighted UniFrac distance: P < 0.001, R2 = 0.025, Bray-curtis dissimilarity: P = 0.045, R2 = 0.011, and Jaccard dissimilarity: P < 0.001, R2 = 0.017) and higher relative abundances of taxa identified by Linear discriminant analysis (LDA) with effect size (Enterococcus, Pedobacter, Massilia, Prevotella_9, Psychrobacter, Butyricimonas, Bradyrhizobium, etc., LDA scores > 2.0) when compared with the control group. The higher pathway abundance of steroid hormone biosynthesis predicted by oral microbiota was suggested to be linked to VEVM (q = 0.020). Further, a model based on oral microbial traits showed good predictive performance for VEVM with an area under the receiver operating characteristic curve of 0.920 (95% confidence interval: 0.834–1.000). Similar results were also obtained between children with etiologically diagnosed VEVM (n = 43) and controls (n = 68). Our preliminary study identified VEVM-specific oral microbial traits among children, which can be effective in the diagnosis of VEVM.

Citations

Citations to this article as recorded by

The microbiota-brain connection in neurological diseases: the ubiquitous short-chain fatty acids
Luisa BERTIN, Erica BONAZZI, Sonia FACCHIN, Greta LORENZON, Daria MANIERO, Caterina DE BARBA, Antonietta TOMASULO, Andrea FORTUNA, Fabiana ZINGONE, Brigida BARBERIO, Edoardo V. SAVARINO
Minerva Gastroenterology.2025;[Epub] CrossRef
Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis
Yi-Long Wang, Xiao-Tong Guo, Meng-Ying Zhu, Yu-Chen Mao, Xue-Bin Xu, Yi Hua, Lu Xu, Li-Hua Jiang, Cong-Ying Zhao, Xin Zhang, Guo-Xia Sheng, Pei-Fang Jiang, Zhe-Feng Yuan, Feng Gao
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef
Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection
William Bourumeau, Karine Tremblay, Guillaume Jourdan, Catherine Girard, Catherine Laprise
Microorganisms.2023; 11(11): 2703. CrossRef

Randomized Controlled Trial

Ulmus macrocarpa Hance extract modulates intestinal microbiota in healthy adults: a randomized, placebo-controlled clinical trial: Kwangmin Kim , Karpagam Veerappan , Nahyun Woo , Bohyeon Park , Sathishkumar Natarajan , Hoyong Chung , Cheolmin Kim , Junhyung Park; J. Microbiol. 2021;59(12):1150-1156. Published online October 26, 2021; DOI: https://doi.org/10.1007/s12275-021-1329-8

354 View
0 Download
6 Web of Science
6 Crossref

Abstract PDF

The stem and root bark of Ulmus macrocarpa Hance has been used as traditional pharmacological agent against inflammation related disorders. The objective of this study was to explore the impact of Ulmus macrocarpa Hance extract (UME) on human gut microbiota. A randomized placebo-controlled clinical study was conducted in healthy adults. The study subjects were given 500 mg/day of UME or placebo orally for 4 weeks. Eighty fecal samples were collected at baseline and 4 weeks of UME or placebo intervention. The gut microbiota variation was evaluated by 16S rRNA profiling. The microbial response was highly personalized, and no statistically significant differences was observed in both species richness and abundance. The number of bacterial species identified in study subjects ranged from 86 to 182 species. The analysis for taxonomical changes revealed an increase in Eubacterium ventriosum, Blautia faecis, Ruminococcus gnavus in the UME group. Functional enrichment of bacterial genes showed an increase in primary and secondary bile acid biosynthesis in UME group. Having known from previous studies Eubacterium regulated bile acid homeostasis in protecting gut microbial architecture and immunity, we suggest that UME supplementation might enhance host immunity by modulating gut microbiota. This is the first stage study and forthcoming clinical studies with larger participants are needed to confirm these findings.

Citations

Citations to this article as recorded by

Catechin and flavonoid glycosides from the Ulmus genus: Exploring their nutritional pharmacology and therapeutic potential in osteoporosis and inflammatory conditions
Chanhyeok Jeong, Chang Hyung Lee, Jiwon Seo, Jung Han Yoon Park, Ki Won Lee
Fitoterapia.2024; 178: 106188. CrossRef
Comparative transcriptomes of four Elm species provide insights into the genetic features and adaptive evolution of Ulmus spp.
Shijie Wang, Lihui Zuo, Yichao Liu, Lianxiang Long, Jianghao Wu, Mengting Yuan, Jinmao Wang, Minsheng Yang
Forest Ecology and Management.2024; 553: 121560. CrossRef
Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial
Oscar de Jesús Calva-Cruz, Cesaré Ovando-Vázquez, Antonio De León-Rodríguez, Fabiola Veana, Eduardo Espitia-Rangel, Samuel Treviño, Ana Paulina Barba-de la Rosa
Foods.2023; 12(14): 2760. CrossRef
Potential lipid-lowering effects of Ulmus macrocarpa Hance extract in adults with untreated high low-density lipoprotein cholesterol concentrations: A randomized double-blind placebo-controlled trial
Ye Li Lee, Sang Yeoup Lee
Frontiers in Medicine.2022;[Epub] CrossRef
Research progress on the relationship between intestinal microecology and intestinal bowel disease
Qianhui Fu, Tianyuan Song, Xiaoqin Ma, Jian Cui
Animal Models and Experimental Medicine.2022; 5(4): 297. CrossRef
The current status of old traditional medicine introduced from Persia to China
Jinmin Shi, Yifan Yang, Xinxin Zhou, Lijun Zhao, Xiaohua Li, Abdullah Yusuf, Mohaddeseh S. M. Z. Hosseini, Fatemeh Sefidkon, Xuebo Hu
Frontiers in Pharmacology.2022;[Epub] CrossRef

Journal Article

Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria: Fuquan Xie , Siwen Niu , Xihuang Lin , Shengxiang Pei , Li Jiang , Yun Tian , Gaiyun Zhang; J. Microbiol. 2021;59(10):886-897. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1186-5

414 View
2 Download
13 Web of Science
14 Crossref

Abstract PDF

We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.

Citations

Citations to this article as recorded by

Identification, evaluation, control of yellow-causing bacteria and their influence on the quality of high moisture rice-based food
Sijie Zhang, Lin Ou, Cuiping Yi, Qiutao Xie, Yang Shan
Food Control.2025; 168: 110887. CrossRef
Microbacterium xanthum sp. nov. Isolated from Seaweed, with the Reclassification of Microbacterium ihumii Yacouba et al. 2023 as a Later Heterotypic Synonym of Microbacterium tenebrionis Lee and Kim 2023
Soon Dong Lee, Hong Lim Yang, In Seop Kim
Current Microbiology.2025;[Epub] CrossRef
Chlamydomonas reinhardtii and Microbacterium forte sp. nov., a mutualistic association that favors sustainable hydrogen production
Neda Fakhimi, María Jesus Torres, Emilio Fernández, Aurora Galván, Alexandra Dubini, David González-Ballester
Science of The Total Environment.2024; 913: 169559. CrossRef
Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers
Mariola Paściak, Krzysztof J. Pawlik, Dariusz Martynowski, Łukasz Łaczmański, Jarosław Ciekot, Bogumiła Szponar, Angelina Wójcik‐Fatla, Barbara Mackiewicz, Ewelina Farian, Grażyna Cholewa, Alicja Cholewa, Jacek Dutkiewicz
Environmental Microbiology Reports.2024;[Epub] CrossRef
Microbacterium aquilitoris sp. nov. and Microbacterium gwkjiense sp. nov., isolated from beach
Soon Dong Lee, Hong Lim Yang, Ji-Sun Kim, In Seop Kim
Archives of Microbiology.2024;[Epub] CrossRef
Microbacterium algihabitans sp. nov., Microbacterium phycohabitans sp. nov., and Microbacterium galbum sp. nov., isolated from dried beach seaweeds
Soon Dong Lee, Hong Lim Yang, In Seop Kim
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone
Marcella D. Baiz, Andrew W. Wood, David P. L. Toews
Proceedings of the Royal Society B: Biological Sciences.2024;[Epub] CrossRef
Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil
Jiawen Zheng, Yunyu Liao, Yang Li, Dongsheng Li, Yaping Sun, Zijun Xiao
Archives of Microbiology.2024;[Epub] CrossRef
Can Sugarcane Yield and Health Be Altered with Fully Mechanized Management?
Jian Xiao, Tian Liang, Shangdong Yang, Hongwei Tan
Agronomy.2023; 13(1): 153. CrossRef
Evaluation of Various Escherichia coli Strains for Enhanced Lycopene Production
Jun Ren, Junhao Shen, Thi Duc Thai, Min-gyun Kim, Seung Ho Lee, Wonseop Lim, Dokyun Na
Journal of Microbiology and Biotechnology.2023; 33(7): 973. CrossRef
Effects of flavonoids on membrane adaptation of food-associated bacteria
Maria Linden, Alexander Flegler, Michelle M. Feuereisen, Fabian Weber, André Lipski, Andreas Schieber
Biochimica et Biophysica Acta (BBA) - Biomembranes.2023; 1865(4): 184137. CrossRef
Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium
Soon Dong Lee, Hong Lim Yang, In Seop Kim
Frontiers in Microbiology.2023;[Epub] CrossRef
Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions
Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer
Microorganisms.2023; 11(1): 170. CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef

Review

[MINIREVIEW]The rapid adaptation of SARS-CoV-2–rise of the variants: transmission and resistance: Sandrine M. Soh , Yeongjun Kim , Chanwoo Kim , Ui Soon Jang , Hye-Ra Lee; J. Microbiol. 2021;59(9):807-818. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1348-5

325 View
0 Download
16 Web of Science
16 Crossref

Abstract PDF

The causative factor of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously mutating. Interestingly, identified mutations mainly occur in the spike (S) protein which interacts with the ACE2 receptor and is cleaved via serine protease TMPRSS2. Some mutated strains are becoming dominant in various parts of the globe because of increased transmissibility as well as cell entry efficacy. Remarkably, the neutralizing activity of monoclonal antibodies, convalescent sera, and vaccines against the variants has been reported to be significantly reduced. Therefore, the efficacy of various monoclonal antibodies therapy and vaccines against these variants is becoming a great global concern. We herein summarize the current status of SARS-CoV- 2 with gears shifted towards the recent and most common genetic variants in relation to transmission, neutralizing activity, and vaccine efficacy.

Citations

Citations to this article as recorded by

Understanding the Molecular Actions of Spike Glycoprotein in SARS-CoV-2 and Issues of a Novel Therapeutic Strategy for the COVID-19 Vaccine
Yasunari Matsuzaka, Ryu Yashiro
BioMedInformatics.2024; 4(2): 1531. CrossRef
Complex vaccination strategies prevent the emergence of vaccine resistance
Simon A Rella, Yuliya A Kulikova, Aygul R Minnegalieva, Fyodor A Kondrashov, Ben Ashby, Tim Connallon
Evolution.2024; 78(10): 1722. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies
Sarah E. Fumagalli, Nigam H. Padhiar, Douglas Meyer, Upendra Katneni, Haim Bar, Michael DiCuccio, Anton A. Komar, Chava Kimchi-Sarfaty
Virology Journal.2023;[Epub] CrossRef
Broad neutralization against SARS-CoV-2 variants induced by ancestral and B.1.351 AS03-Adjuvanted recombinant Plant-Derived Virus-Like particle vaccines
Charlotte Dubé, Sarah Paris-Robidas, Guadalupe Andreani, Cindy Gutzeit, Marc-André D'Aoust, Brian J. Ward, Sonia Trépanier
Vaccine.2022; 40(30): 4017. CrossRef
A tentative tracking of the SARS-Cov2 pandemic in France, based on a corrected SIR model including vaccination effects
Mathilde Varret, François Xavier Martin, François Varret, J.-C.S. Lévy
EPJ Web of Conferences.2022; 263: 01002. CrossRef
Changing Dynamics of SARS-CoV-2: A Global Challenge
Ananya Chugh, Nimisha Khurana, Kangna Verma, Ishita Sehgal, Rajan Rolta, Pranjal Vats, Rajendra Phartyal, Deeksha Salaria, Neha Kaushik, Eun Ha Choi, Mansi Verma, Nagendra Kumar Kaushik
Applied Sciences.2022; 12(11): 5546. CrossRef
The SARS-CoV-2 differential genomic adaptation in response to varying UVindex reveals potential genomic resources for better COVID-19 diagnosis and prevention
Naveed Iqbal, Muhammad Rafiq, Masooma, Sanaullah Tareen, Maqsood Ahmad, Faheem Nawaz, Sumair Khan, Rida Riaz, Ting Yang, Ambrin Fatima, Muhsin Jamal, Shahid Mansoor, Xin Liu, Nazeer Ahmed
Frontiers in Microbiology.2022;[Epub] CrossRef
SARS-CoV-2 Variants of Concern Hijack IFITM2 for Efficient Replication in Human Lung Cells
Rayhane Nchioua, Annika Schundner, Dorota Kmiec, Caterina Prelli Bozzo, Fabian Zech, Lennart Koepke, Alexander Graf, Stefan Krebs, Helmut Blum, Manfred Frick, Konstantin M. J. Sparrer, Frank Kirchhoff, Tom Gallagher
Journal of Virology.2022;[Epub] CrossRef
Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants
Severino Jefferson Ribeiro da Silva, Suelen Cristina de Lima, Ronaldo Celerino da Silva, Alain Kohl, Lindomar Pena
Frontiers in Medicine.2022;[Epub] CrossRef
Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants
Lili Li, Meiling Gao, Peng Jiao, Shulong Zu, Yong-qiang Deng, Dingyi Wan, Yang Cao, Jing Duan, Saba R Aliyari, Jie Li, Yueyue Shi, Zihe Rao, Cheng-feng Qin, Yu Guo, Genhong Cheng, Heng Yang
Cell & Bioscience.2022;[Epub] CrossRef
Perspectives and Factors Affecting the Preventive Behavior Pertinent to COVID-19 among School Employees in Chiang Mai, Thailand: A Cross-Sectional Study
Pheerasak Assavanopakun, Tharntip Promkutkao, Suchat Promkutkeo, Wachiranun Sirikul
International Journal of Environmental Research and Public Health.2022; 19(9): 5662. CrossRef
Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial
Karin Hardt, An Vandebosch, Jerald Sadoff, Mathieu Le Gars, Carla Truyers, David Lowson, Ilse Van Dromme, Johan Vingerhoets, Tobias Kamphuis, Gert Scheper, Javier Ruiz-Guiñazú, Saul N Faust, Christoph D Spinner, Hanneke Schuitemaker, Johan Van Hoof, Macay
The Lancet Infectious Diseases.2022; 22(12): 1703. CrossRef
Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions
Denis Jacob Machado, Richard Allen White, Janice Kofsky, Daniel A. Janies
Antimicrobial Stewardship & Healthcare Epidemiology.2021;[Epub] CrossRef
Daily Physical Activity and Sleep Measured by Wearable Activity Trackers during the Coronavirus Disease 2019 Pandemic: A Lesson for Preventing Physical Inactivity during Future Pandemics
Hidetaka Hamasaki
Applied Sciences.2021; 11(21): 9956. CrossRef
The adaptation of SARS-CoV-2 to humans
Eduardo Tosta
Memórias do Instituto Oswaldo Cruz.2021;[Epub] CrossRef

Journal Articles

UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis: Jihyeon Kim , Seong-In Na , Dongwook Kim , Jongsik Chun; J. Microbiol. 2021;59(6):609-615. Published online May 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1231-4

446 View
0 Download
186 Web of Science
172 Crossref

Abstract PDF

Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2.

Citations

Citations to this article as recorded by

Proposal of Lactococcus intestinalis Sun et al. 2024 as a Later Heterotypic Synonym of Lactococcus muris Afrizal et al. 2023
Xin-Yu Zhu, Chun Tao Gu
Current Microbiology.2025;[Epub] CrossRef
Genomic insights into drug resistance and virulence determinants in rare pyomelanin-producing clinical isolates of Acinetobacter baumannii
Lipsa Panda, Krishnapriya GK, Ajit Ramesh Sawant, Santosh Kumar Singh, Minakshi Gupta, Sheela Devi C, P Shashikala, K Prashanth
European Journal of Clinical Microbiology & Infectious Diseases.2025; 44(3): 533. CrossRef
Taxonomic and genomic characterization of a siderophore-producing bacterium, Rhodoligotrophos ferricapiens sp. nov isolated from lettuce cultivation soil
Yu-Jin Kim, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge
Miku Takahashi, Kanata Hoshino, Moriyuki Hamada, Tomohiko Tamura, Ryota Moriuchi, Hideo Dohra, Youji Nakagawa, Susumu Kokubo, Motoyuki Yamazaki, Hiroyuki Nakagawa, Masayuki Hayakawa, Shinya Kodani, Hideki Yamamura
The Journal of Antibiotics.2025; 78(1): 35. CrossRef
Proposal of Crystallibacter gen. nov., Crystallibacter permensis sp. nov. and Crystallibacter degradans sp. nov. for the salt-tolerant and aromatics degrading actinobacteria, and reclassification of Arthrobacter crystallopoietes as Crystallibacter crystal
Elena G. Plotnikova, Elena V. Ariskina, Olga V. Yastrebova, Natalia V. Potekhina, Alexander N. Avtukh, Sergey V. Tarlachkov, Irina P. Starodumova, Lyubov V. Dorofeeva, Lyudmila I. Evtushenko
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Description and genomic characterization of Mangrovibrevibacter kandeliae gen. nov. sp. nov., a novel carotenoid-producing endophytic bacterium isolated from branch of mangrove plants
Chengshao Zan, Zhouqing Zheng, Xiaohui Chen, Mingsheng Chen, Feina Li, Li Tuo
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer)
Shuan Er, Melissa Soh, Adrian Low, Henning Seedorf
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Phenotypic and Complete Reference Whole Genome Sequence Analyses of Two Paenibacillus spp. Isolates from a Gray Wolf (Canis lupus) Gastrointestinal Tract
Jessika L. Bryant, Jennifer McCabe, C. Cristoph Klews, MiCayla Johnson, Ariel N. Atchley, Thomas W. Cousins, Maya Barnard-Davidson, Kristina M. Smith, Mark R. Ackermann, Michael Netherland, Nur A. Hasan, Peter A. Jordan, Evan S. Forsythe, Patrick N. Ball,
Veterinary Sciences.2025; 12(1): 51. CrossRef
Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues
Leonor Matos, Lorrie Maccarrio, Ana Paula Chung, Diogo N. Proença, Søren Sørensen, Paula V. Morais, Romeu Francisco
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov., two bacteria isolated from marine sediment in the East China Sea
Hao Wang, Huiting Wang, Xinyu Liu, Dawoon Jung, Eun-Young Seo, Shan He, Weiyan Zhang, Lijian Ding
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Paenibacillus mesotrionivorans sp. nov., a Mesotrione-Degrading Strain Isolated from Soil
Ye Song, Yan Wu, Leyao Chen, Luyao Ruan, Minglai Wan, Bin Liu, Jian He, Baolong Zhang
Current Microbiology.2025;[Epub] CrossRef
Genomic and phenotypic characterisation of Leeuwenhoekiella obamensis sp. nov., a novel marine bacterium isolated from the surface water of a Japanese fishing port
Yuka Machii, Mao Tsukamoto, Takafumi Kataoka, Ryuji Kondo
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Comamonas halotolerans sp. nov., isolated from the faecal sample of a zoo animal, Naemorhedus caudatus
Yerim Park, Bitnara Kim, Jihyeon Min, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Gallibacterium faecale sp. nov., Isolated from Dairy Cow Feces
Seoung Woo Ryu, Jeong Chan Moon, Byeong Seob Oh, Seung Yeob Yu, Jeong Eun Bak, Eun Seo Heo, Seung-Hwan Park, Se Won Kang, Jiyoung Lee, Mi-Kyung Lee, Mooyoung Jung, Yo Han Choi, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee
Current Microbiology.2025;[Epub] CrossRef
Reference Whole Genome Sequence Analyses and Characterization of a Novel Carnobacterium maltaromaticum Distinct Sequence Type Isolated from a North American Gray Wolf (Canis lupus) Gastrointestinal Tract
C. Cristoph Klews, Jessika L. Bryant, Jennifer McCabe, Ariel N. Atchley, Thomas W. Cousins, Maya Barnard-Davidson, Mark R. Ackermann, Michael Netherland, Nur A. Hasan, Peter A. Jordan, Evan S. Forsythe, Patrick N. Ball, Bruce S. Seal
Veterinary Sciences.2025; 12(5): 410. CrossRef
Genomic diversity and tracing of Paenibacillus larvae in Australia: implications for American foulbrood outbreak surveillance in low-diversity populations
Paul Worden, Ashlea Webster, Khushbu Gandhi, Risha Gupta, Ania T. Deutscher, Michael Hornitzky, Daniel Ross Bogema
Microbial Genomics .2025;[Epub] CrossRef
Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A
Geoffrey Masuyer, Alistair Taverner, Julia MacKay, Ana Rita Lima Marques, Yuye Wang, Tom Hunter, Keyi Liu, Randall J. Mrsny
Communications Biology.2025;[Epub] CrossRef
Biocontrol Effect of Bacillus velezensis D7-8 on Potato Common Scab and Its Complete Genome Sequence Analysis
Yu Jiang, Pengfei He, Huihui Kong, Pengbo He, Yixin Wu, Guowen Tang, Ping Tang, Yining Di, Xingyu Li, Lufeng Liu, Shahzad Munir, Yueqiu He
Microorganisms.2025; 13(4): 770. CrossRef
House dust microbiome differentiation and phage-mediated antibiotic resistance and virulence dissemination in the presence of endocrine-disrupting chemicals and pharmaceuticals
Shicong Du, Huiju Lin, Qiong Luo, Chung Ling Man, Sze Han Lai, Kin Fai Ho, Kenneth M. Y. Leung, Patrick K. H. Lee
Microbiome.2025;[Epub] CrossRef
Fulvimarina uroteuthidis sp. nov., isolated from a marine invertebrate and Uroteuthis (Photololigo) edulis
Yea-Lin Moon, Kyung Hyun Kim, Jin-Sook Park
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Metabolic response of tellurite resistant Bacillus altitudinis strain 3W19 highlights the potential as a model organism for bioremediation
Pedro Farias, Romeu Francisco, Lorrie Maccario, Jakob Herschend, Søren J. Sørensen, Paula V. Morais
Scientific Reports.2025;[Epub] CrossRef
Reclassification of Bifidobacterium faecale Choi et al. 2014 as a later heterotypic synonym of Bifidobacterium adolescentis Reuter 1963
Shinnosuke Okuhama, Hidenori Takahashi, Yasunori Nakayama, Akihito Endo
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Taxonomic revision of the family Aurantimonadaceae: proposal of Dennerimonas gen. nov., Mesocryomonas gen. nov., Rathsackimonas gen. nov. and Plantimonas gen. nov., along with the reclassification of Jeongeupella Jiang et al. 2024 as a later heterotypic s
Imed Sbissi, Hana Dali, Rihab Hamra, Emeni Boujemaa, Mohamed Aziz Haj Nasr, Faten Ghodhbane-Gtari, Maher Gtari
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Phylogenomics as baseline for taxonomy description: Amphibiibacter pelophylacis gen. nov., sp. nov., a novel taxon of the family Sphaerotilaceae, class Betaproteobacteria, isolated from the skin microbiota of Pelophylax perezi from different populations
Sara Costa, Diogo Neves Proença, Isabel Lopes, Paula V. Morais
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Description of Flavobacterium fructosi sp. nov., Flavobacterium xylosi sp. nov. and Flavobacterium zhouii sp. nov., three new members of the genus Flavobacterium
Dou Han, Lei-Lei Yang, Yu-Hua Xin, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Enterococcus hailinensis sp. nov., Isolated from Traditional Chinese Pickle
Ting-Yu Wang, Hao Wang, Chun Tao Gu
Current Microbiology.2025;[Epub] CrossRef
Genome-guided development of a bacterial two-strain system for low-temperature soil biocementation
Karol Ciuchcinski, Grzegorz Czerwonka, Przemyslaw Decewicz, Zofia Godlewska, Katarzyna Misiolek, Katarzyna Zegadlo, Michal Styczynski, Lukasz Dziewit
Applied Microbiology and Biotechnology.2025;[Epub] CrossRef
Familial Reclassification Within Order Lysobacterales and Proposal of Four Novel Species
Tengfei Ma, Haijiao Liu, Yafei Chen, Juan Liu, Chungen Piao, Han Xue, Risheng Xu, Yong Li
Microorganisms.2025; 13(6): 1212. CrossRef
Draft genome sequences of Thermus thermophilus strains isolated from Japanese hot springs
Yu Sato, Masanori Hashino, Shintaro Maeno, Elinne Becket
Microbiology Resource Announcements.2025;[Epub] CrossRef
Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ
Jun Bae Park, Gwanwoo Lee, Yu-Yeon Han, Dongwook Kim, Kyoo Heo, Jeesoo Kim, Juhee Park, Hyosuk Yun, Chul Won Lee, Hyun-Soo Cho, Jong-Seo Kim, Martin Steinegger, Yeong-Jae Seok, Soung-Hun Roh
Proceedings of the National Academy of Sciences.2025;[Epub] CrossRef
Lacticaseibacillus suihuaensis sp. nov., Isolated from Traditional Chinese Pickle
Xin-Yu Zhu, Chun Yan Li, Hao Wang, Chun Tao Gu
Current Microbiology.2025;[Epub] CrossRef
Idiomarina aminovorans sp. nov., a halophilic bacterium isolated from the Llamara salt pan in the Atacama Desert of northern Chile
Christian Hintersatz, Luis Antonio Rojas, Sean Ting-Shyang Wei, Sabine Kutschke, Angela Thewes, Falk Lehmann, Rohan Jain, Katrin Pollmann
Extremophiles.2025;[Epub] CrossRef
Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains
Sara Jordan, Joël F. Pothier, Pieter de Maayer, Kirk Broders, Brian H. Kvitko, Teresa A. Coutinho, Theo H. M. Smits
BMC Microbiology.2025;[Epub] CrossRef
Single cell viral tagging of Faecalibacterium prausnitzii reveals rare bacteriophages omitted by other techniques
Danielle E. Campbell, Xiaofen Wu, Lindsey R. Hall, Dylan Lawrence, Jerome M. Molleston, Lawrence A. Schriefer, Lindsay Droit, James S. Weagley, Benjamin S. Olson, Joanna Rimmer, Miles Parkes, Scott A. Handley, Megan T. Baldridge
Gut Microbes.2025;[Epub] CrossRef
Lacticaseibacillus salsurae sp. nov. and Levilactobacillus muriae sp. nov., isolated from traditional Chinese pickle
Si-Tong Song, Ting-Yu Wang, Xin-Yu Zhu, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Taxonomic rearrangement of Salinibacterium, Leifsonia, Diaminobutyricibacter, Antiquaquibacter, Homoserinimonas and Glaciibacter: refining genus boundaries and proposal of two new genera – Orlajensenia gen. nov. and Leifsonella gen. nov.
Maher Gtari, Dhouha Boussoufa, Faten Ghodhbane-Gtari, Imed Sbissi
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov., isolated from human feces, and the reclassification of Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Egg
Ah-In Yang, Bora Kim, Woorim Kang, Hae-In Joe, Na-Ri Shin
Journal of Microbiology.2025; 63(6): e2502006. CrossRef
Pseudomonas lyxosi sp. nov., Pseudomonas arabinosi sp. nov. and Pseudomonas frigoris sp. nov., isolated from glaciers
Chan Zhao, Yu-Hua Xin, Qing Liu
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Paenibacillus nanchangensis sp. nov., a Nitrogen-Fixing Strain Isolated from Agricultural Soil
Yan Wu, Leyun Dong, Bingbing Weng, Xiaozhen Shi, Ningning Wu, Jian He, Zongzhuan Shen, Jiandong Jiang, Qirong Shen
Current Microbiology.2025;[Epub] CrossRef
Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes
Dongwook Kim, Sukhwan Park, Martin Steinegger, Caroline zz Puente-Lelievre
Genome Biology and Evolution.2025;[Epub] CrossRef
Haloimpatiens sporogenes sp. nov. and Haloimpatiens myeolchijeotgali sp. nov., anaerobic bacteria isolated from Myeolchi-jeot, a traditional Korean fermented anchovy
Yu Jeong Lee, Byung Hee Chun
Journal of Microbiology.2025; 63(7): e2504009. CrossRef
Ewingella docleensis sp. nov. isolated from artisanal Montenegrin komanski cheese
Beatriz Daza Prieto, Nadja Raicevic, Patrick Hyden, Adriana Cabal, Johann Ladstätter, Susanne Richter, Anna Stoeger, Robert L. Mach, Aleksandra Martinovic, Werner Ruppitsch
The Microbe.2025; 8: 100449. CrossRef
Faecalibacterium langellae sp. nov. isolated from human faeces
Adeline Ang, Véronique Robert, Atsushi Hisatomi, Masahiro Hirasaki, Shintaro Maeno, Moriya Ohkuma, Mitsuo Sakamoto, Jean-Marc Chatel, Akihito Endo
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Genome-based reclassification of the genus Lactococcus and two novel species Pseudolactococcus yaeyamensis gen. nov., sp. nov. and Lactovum odontotermitis sp. nov. isolated from the gut of termites
Kota Abe, Masahiro Yuki, Yumiko Imagawa, Atsushi Hisatomi, Moriya Ohkuma, Mitsuo Sakamoto, Satoko Noda
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Genome-Wide Insights into Streptomyces Novel Species Qhu-G9 and Its Potential for Enhancing Salt Tolerance and Growth in Avena sativa L. and Onobrychis viciifolia Scop
Xin Xiang, Xiaolan Ma, Hengxia Yin, Liang Chen, Jiao Li, Wenjing Li, Shuhan Zhang, Chenghang Sun, Benyin Zhang
Plants.2025; 14(14): 2135. CrossRef
Bradyrhizobium tunisiense sp. nov., a novel rhizobial species isolated from Acacia saligna nodules
Jihed Hsouna, Houda Zouagui, Takwa Gritli, Houda Ilahi, Jia-Cheng Han, Muhammad Sulman, Walid Ellouze, Xiao Xia Zhang, Maroua Mansouri, Mustapha Missbah El Idrissi, Soufiane Alami, Pierre Emmanuel Courty, Daniel Wipf, Abdelkader Bekki, James T. Tambong, B
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Distribution of Iron Importers and Ecological Traits in Pseudomonas Species Highlights the Potential Role of Efe System in Plant‐Related Environments
Kenji Okumura, Kohei Ogura, Wataru Hashimoto
Environmental Microbiology.2025;[Epub] CrossRef
Genetic Characterization and Symbiotic Performance of Soybean Rhizobia Under Cold and Water-Deficient Conditions in Poland
Riku Watanabe, Maria Daniela Artigas Ramirez, Shin-ichiro Agake, Sonoko Dorothea Bellingrath-Kimura, Sylwia Lewandowska, Yuki Onishi, Yohei Nishikawa, Haruko Takeyama, Michiko Yasuda, Naoko Ohkama-Ohtsu
Plants.2025; 14(12): 1786. CrossRef
The Isolation and Characterization of a Novel Psychrotolerant Cellulolytic Bacterium, Microbacterium sp. QXD-8T
Peng An, Changjialian Yang, Wei Li, Dahe Zhao, Hua Xiang
Microorganisms.2024; 12(2): 303. CrossRef
Isolation of highly copper-resistant bacteria from deep-sea hydrothermal fields and description of a novel species Marinobacter metalliresistant sp. nov
Tong Yu, Meng Qin, Zongze Shao, Yuemei Zhao, Xiang Zeng
Frontiers in Microbiology.2024;[Epub] CrossRef
Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum
Sylvia I. Chi, Mercy Akuma, Renlin Xu, Véronique Plante, Mehri Hadinezhad, James T. Tambong
Scientific Reports.2024;[Epub] CrossRef
Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes
Munisamy Prathaban, Ragothaman Prathiviraj, Mythili Ravichandran, Sharmila Devi Natarajan, Murugesan Sobanaa, S. Hari Krishna Kumar, Varadharaju Chandrasekar, Joseph Selvin
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil
Cheng-Jie Xie, Ling Yao, Rong Tang, Shuang Han, Shang Yang, Hend Alwathnani, Christopher Rensing, Guo-Hong Liu, Shun-Gui Zhou
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Veillonella faecalis sp. nov., a propionic acid-producing bacterium isolated from the faeces of an infant
Haneol Yang, Hana Jo, Seung Hyun Kim, Chan-Seok Yun, Seung-Hwan Park, Doo-Sang Park
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils
Flor N. Rivera Ortuña, Joseph Guevara-Luna, Jun Yan, Eloisa Lopez Amezcua, Ivan Arroyo-Herrera, Yan Li, Maria Soledad Vásquez-Murrieta, Danae Rojas Arellano, En Tao Wang
Archives of Microbiology.2024;[Epub] CrossRef
Chitiniphilus purpureus sp. nov., a novel chitin-degrading bacterium isolated from crawfish pond sediment
Kaiyang Li, Xiong Luo, Rongrong Fan, Zhuoran Ding, Shixue Zheng, Zhengjun Chen
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Augmenting bacterial similarity measures using a graph-based genome representation
Vivek Ramanan, Indra Neil Sarkar, Sergio Baranzini
mSystems.2024;[Epub] CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
The genome of a new Halorubrum distributum strain ICIS4 isolated from the culture of a microalga Dunaliella salina
Е. А. Selivanova, А. S. Balkin, Yu. А. Khlopko, V. Ya. Kataev, А. О. Plotnikov
Microbiology.2024; 93(4): 444. CrossRef
Biological Control of Streptomyces sp. PR69 Against Phytophthora capsici and Its Growth-Promoting Effects on Plants
Perla Karina López-Reyes, Susana De la Torre-Zavala, María Mercedes Cortés-González, Luis Jesús Galán-Wong, Hamlet Avilés-Arnaut
Horticulturae.2024; 10(12): 1365. CrossRef
Pectobacterium punjabense Causing Blackleg and Soft Rot of Potato: The First Report in the Russian Federation
Anna A. Vasilyeva, Peter V. Evseev, Alexandr N. Ignatov, Fevzi S.-U. Dzhalilov
Plants.2024; 13(15): 2144. CrossRef
Taxonogenomic analysis of the Xanthomonas translucens complex leads to the descriptions of Xanthomonas cerealis sp. nov. and Xanthomonas graminis sp. nov.
James T. Tambong, Renlin Xu, Maria Constanza Fleitas, Randy Kutcher
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov.
Soo-Bin Kim, Kyung Hyun Kim, Jin-Sook Park
Current Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Analysis of Whole-Genome facilitates rapid and precise identification of fungal species
Guihong Qi, Lijun Hao, Tianyi Xin, Yutong Gan, Qian Lou, Wenjie Xu, Jingyuan Song
Frontiers in Microbiology.2024;[Epub] CrossRef
Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase
Jachym Suman, Kamila Sredlova, Serena Fraraccio, Martina Jerabkova, Michal Strejcek, Hana Kabickova, Tomas Cajthaml, Ondrej Uhlik
Chemosphere.2024; 349: 140909. CrossRef
Commensalibacter nepenthis sp. nov. and Commensalibacter oyaizuii sp. nov., from fluid in a Nepenthes pitcher cup and a butterfly (Junonia lemonias) in Thailand
Pattaraporn Yukphan, Piyanat Charoenyingcharoen, Supattra Muangham, Wuttichai Mhuantong, Yuzo Yamada
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov., and Streptococcus parasalivarius sp. nov., isolated from Traditional Chinese Pickle
Ting-Yu Wang, Chun Yan Li, Hao Wang, Chun Tao Gu
Current Microbiology.2024;[Epub] CrossRef
Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions
Dae Gyu Choi, Ju Hye Baek, Dong Min Han, Shehzad Abid Khan, Che Ok Jeon
BMC Genomics.2024;[Epub] CrossRef
Staphylococcus hsinchuensis sp. nov., Isolated from Soymilk
Yu-Ting Wang, Yu-Chun Lin, Yi-Huei Hsieh, Yu-Tzu Lin, Moriyuki Hamada, Chih-Chieh Chen, Jong-Shian Liou, Ai-Yun Lee, Wei-Ling Zhang, Yung-Tsung Chen, Chien-Hsun Huang
Pathogens.2024; 13(4): 343. CrossRef
Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Rhizobium aouanii sp. nov., efficient nodulating rhizobia isolated from Acacia saligna roots in Tunisia
Jihed Hsouna, Takwa Gritli, Houda Ilahi, Jia-Cheng Han, Walid Ellouze, Xiao Xia Zhang, Maroua Mansouri, Praveen Rahi, Mustapha Missbah El Idrissi, Mouad Lamrabet, Pierre Emmanuel Courty, Daniel Wipf, Abdelkader Bekki, James T. Tambong, Bacem Mnasri
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus
Keisuke Kawano, Tatsuya Awano, Arata Yoshinaga, Junji Sugiyama, Shigeki Sawayama, Satoshi Nakagawa
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Characterization and Genomic Analysis of Affinirhizobium gouqiense sp. nov. Isolated from Seawater of Gouqi Island Located in the East China Sea and Reclassification of Rhizobium lemnae to the Genus Affinirhizobium as Affinirhizobium lemnae comb. nov.
Min He, Gen Chen, Ke-Jing Li, Xing-Xing Tang, Xiao-Xiao Liu, Chang-Bin Ren, Hou-Hong Liu, Hai Luo, Sanjit Chandra Debnath, Pin-Mei Wang, Hai-Xin Chen, Dao-Qiong Zheng
Current Microbiology.2024;[Epub] CrossRef
Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human
Feng-Lan Liu, Rashidin Abdugheni, Cong-Guo Ran, Nan Zhou, Shuang-Jiang Liu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic
Ana Catalina Lara, Lucie Kotrbová, Moritz Keller, Imen Nouioui, Meina Neumann-Schaal, Yvonne Mast, Alica Chroňáková
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Rhodoferax potami sp. nov. and Rhodoferax mekongensis sp. nov., isolated from the Mekong River in Thailand
Supattra Kitikhun, Piyanat Charoenyingcharoen, Paopit Siriarchawatana, Somsak Likhitrattanapisal, Thanyakorn Nilsakha, Amonwan Chanpet, Sukanya Jeennor, Pattaraporn Yukphan, Supawadee Ingsriswang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Thalassotalea aquiviva sp. nov., and Thalassotalea maritima sp. nov., Isolated from Seawater of the Coast in South Korea
Jina Lee, Seung-Hui Song, Kira Moon, Nakyeong Lee, Sangdon Ryu, Hye Seon Song, Sung Moon Lee, Yun Ji Kim, Se Won Chun, Kyung-Min Choi, Aslan Hwanhwi Lee
Journal of Microbiology.2024; 62(12): 1099. CrossRef
Genome Sequencing Unveils Nomadic Traits of Lactiplantibacillus plantarum in Japanese Post-Fermented Tea
Kyoka Sato, Yuichiro Ikagawa, Ryo Niwa, Hiroki Nishioka, Masanori Horie, Hitoshi Iwahashi
Current Microbiology.2024;[Epub] CrossRef
Effects of Limosilactobacillus reuteri strains PTA-126787 and PTA-126788 on intestinal barrier integrity and immune homeostasis in an alcohol-induced leaky gut model
Dharanesh Gangaiah, Min Gu, Aline Zaparte, Olaf Will, Laurie C. Dolan, Anthony Goering, Jason Pillai, Shrinivasrao P. Mane, German Plata, Emily B. Helmes, David A. Welsh, Arvind Kumar Mahajan
Scientific Reports.2024;[Epub] CrossRef
Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota
Nancy O. Nou, Jonathan K. Covington, Dengxun Lai, Xavier Mayali, Cale O. Seymour, Juliet Johnston, Jian-Yu Jiao, Steffen Buessecker, Damon Mosier, Alise R. Muok, Nicole Torosian, Allison M. Cook, Ariane Briegel, Tanja Woyke, Emiley Eloe-Fadrosh, Nicole Sh
Nature Communications.2024;[Epub] CrossRef
Isolation of Sphingopyxis kveilinensis sp. nov., a Potential Antibiotic-Degrading Bacterium, from a Karst Wetland
Ying Chen, Jie Deng, Chengjian Yu
Current Microbiology.2024;[Epub] CrossRef
Transmission and Persistence of Infant Gut-Associated Bifidobacteria
Margaret A. Hilliard, David A. Sela
Microorganisms.2024; 12(5): 879. CrossRef
The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum
Cheng-Shan Jiang, Chun Yan Li, Chun Tao Gu
Current Microbiology.2024;[Epub] CrossRef
Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef
Faecalibacterium taiwanense sp. nov., isolated from human faeces
Jong-Shian Liou, Wei-Ling Zhang, Li-Wen Hsu, Chih-Chieh Chen, Yu-Ting Wang, Koji Mori, Kohei Hidaka, Moriyuki Hamada, Lina Huang, Koichi Watanabe, Chien-Hsun Huang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Mesorhizobium retamae sp. nov., a novel non-nodulating and non-nitrogen-fixing species isolated from the root nodules of Retama raetam sampled in Tunisia
Roukaya Ben Gaied, Imed Sbissi, Mohamed Tarhouni, Katharina Huber, Jacqueline Wolf, Meina Neumann-Schaal, Imen Nouioui, Faten Ghodhbane-Gtari, Maher Gtari
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean
Xavier Rey-Velasco, Teresa Lucena, Ana Belda, Josep M. Gasol, Olga Sánchez, David R. Arahal, María J. Pujalte
Frontiers in Microbiology.2024;[Epub] CrossRef
Lacticaseibacillus jixiensis sp. nov., Isolated from Traditional Chinese Pickle
Si-Tong Song, Chun Yan Li, Chun Tao Gu
Current Microbiology.2024;[Epub] CrossRef
Paracoccus spongiarum sp. nov., isolated from the marine sponge, Phakellia elegans
Soo-Bin Kim, Kyung Hyun Kim, Jin-Sook Park
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis
Yi-Ting Lu, Yi-Yi Wu, Ya-Nan Li, Wei-Yi Zheng, Wen-Zheng Liu
Archives of Microbiology.2024;[Epub] CrossRef
The Genome of a New Halorubrum distributum Strain ICIS4 Isolated from the Culture of a Microalga Dunaliella salina
E. A. Selivanova, A. S. Balkin, Yu. A. Khlopko, V. Ya. Kataev, A. O. Plotnikov
Microbiology.2024; 93(4): 482. CrossRef
Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome
Gagandeep Jaiswal, Rekha Rana, Praveen Kumar Nayak, Rekha Chouhan, Sumit G. Gandhi, Hitendra K. Patel, Prabhu B. Patil
Current Microbiology.2024;[Epub] CrossRef
Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria
Wouter B. Lenferink, Theo A. van Alen, Mike S. M. Jetten, Huub J. M. Op den Camp, Maartje A. H. J. van Kessel, Sebastian Lücker
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Analysis of Whole-Genome for Identification of Seven Penicillium Species with Significant Economic Value
Yuanhao Huang, Lianguo Fu, Yutong Gan, Guihong Qi, Lijun Hao, Tianyi Xin, Wenjie Xu, Jingyuan Song
International Journal of Molecular Sciences.2024; 25(15): 8172. CrossRef
Jatrophihabitans cynanchi sp. nov., isolated from rhizosphere soil of Cynanchum wilfordii
Min Kuk Suh, Ji-Sun Kim, Mi Kyung Eom, Han Sol Kim, Hyo Eun Do, Yong Kook Shin, Jung- Sook Lee
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney
Urara Miyazaki, Daiki Mizutani, Yurina Hashimoto, Akihiro Tame, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Patterns of Change in Nucleotide Diversity Over Gene Length
Farhan Ali, Brian Golding
Genome Biology and Evolution.2024;[Epub] CrossRef
SeqCode facilitates naming of South African rhizobia left in limbo
Melandré van Lill, Stephanus N. Venter, Esther K. Muema, Marike Palmer, Wai Y. Chan, Chrizelle W. Beukes, Emma T. Steenkamp
Systematic and Applied Microbiology.2024; 47(2-3): 126504. CrossRef
Bifidobacterium apicola sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting-Yu Wang, Hao Wang, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis
Jana Schwarzerova, Michal Zeman, Vladimir Babak, Katerina Jureckova, Marketa Nykrynova, Margaret Varga, Wolfram Weckwerth, Monika Dolejska, Valentine Provaznik, Ivan Rychlik, Darina Cejkova, Feng Gao, Johannes Wöstemeyer, Shay Tal, Alejandro Piña-Iturbe,
Microbiology Spectrum.2024;[Epub] CrossRef
Host genetic regulation of human gut microbial structural variation
Daria V. Zhernakova, Daoming Wang, Lei Liu, Sergio Andreu-Sánchez, Yue Zhang, Angel J. Ruiz-Moreno, Haoran Peng, Niels Plomp, Ángela Del Castillo-Izquierdo, Ranko Gacesa, Esteban A. Lopera-Maya, Godfrey S. Temba, Vesla I. Kullaya, Sander S. van Leeuwen, R
Nature.2024; 625(7996): 813. CrossRef
Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation
Nadia Sufdar Ali, Subarna Thakur, Mengwei Ye, Fanny Monteil-Rivera, Youlian Pan, Wensheng Qin, Trent Chunzhong Yang
BMC Microbiology.2024;[Epub] CrossRef
Taxonomic note on Kocuria and Rothia: taxogenomic insights for addressing misidentifications and proposing new combinations and new subspecies
Faten Ghodhbane-Gtari, Mohamed Aziz Haj Nasr, Rafik Gatri, Maher Gtari
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella
Yea-Lin Moon, Kyung Hyun Kim, Jin-Sook Park
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Adlercreutzia faecimuris sp. nov., producing propionate and acetate isolated from mouse feces
Min Kuk Suh, Jong- Sik Jin, Hyo Eun Do, Ji-Sun Kim, Mi Kyung Eom, Han Sol Kim, Jung- Sook Lee
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material
Xiaodong Liu, Xin Liu, Zhenshan Deng, Xiaolong He, Yingying Jiang
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Kribbella caucasensis sp. nov. from the Soil of the North Caucasus Mountains
A. N. Avtukh, E. V. Ariskina, L. M. Baryshnikova, N. V. Prisyazhnaya, L. V. Dorofeeva, L. I. Evtushenko
Microbiology.2024; 93(6): 730. CrossRef
Peptostreptococcus equinus sp. nov., isolated from horse faeces
Hye Su Jung, Jeong Ui Yun, Mi-Ja Jung, Hye Seon Song, Yeon Bee Kim, Yujin Kim, Min Ji Lee, Jisu Lee, Che Ok Jeon, Seong Woon Roh, Tae Woong Whon, Joon-Gyu Kim, Se Hee Lee
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Aurantiacibacter poecillastricola sp. nov., Isolated from the Marine Sponge, Poecillastra wondoensis, and Reclassification of Erythrobacter alti as Aurantiacibacter alti comb. nov.
Soo-Bin Kim, Kyung Hyun Kim, Jin-Sook Park
Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts
Tomoaki Kouya, Yohei Ishiyama, Shota Ohashi, Ryota Kumakubo, Takeshi Yamazaki, Toshiki Otaki, Guadalupe Virginia Nevárez-Moorillón
PLOS ONE.2023; 18(6): e0286677. CrossRef
Comparative Genomic Analysis and BTEX Degradation Pathways of a Thermotolerant Cupriavidus cauae PHS1
Chandran Sathesh-Prabu, Jihoon Woo, Yuchan Kim, Suk Min Kim, Sun Bok Lee, Che Ok Jeon, Donghyuk Kim, Sung Kuk Lee
Journal of Microbiology and Biotechnology.2023; 33(7): 875. CrossRef
Complete genome sequence of the emerging pathogen Cysteiniphilum spp. and comparative genomic analysis with genus Francisella : Insights into its genetic diversity and potential virulence traits
Changrui Qian, Mengxin Xu, Zeyu Huang, Miran Tan, Cheng Fu, Tieli Zhou, Jianming Cao, Cui Zhou
Virulence.2023;[Epub] CrossRef
Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov., isolated from seawater
Sylvia Kristyanto, Jaejoon Jung, Jeong Min Kim, Byeong Jun Choi, Dong Min Han, Sung Chul Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Atopomonas sediminilitoris sp. nov., isolated from beach sediment of Zhairuo Island, China
Kejing Li, Zhenbo Ye, Gen Chen, Kaiwen Zheng, Jun Yin, Sanjit Chandra Debnath, Cen Yan, Yi Hong, Zhen Guo, Pinmei Wang, Fabai Wu, Daoqiong Zheng
Antonie van Leeuwenhoek.2023; 116(2): 97. CrossRef
Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea
Miryung Kim, Yong-Seok Kim, Chang-Jun Cha
Journal of Microbiology.2023; 61(1): 37. CrossRef
Paenibacillus soyae sp. nov., isolated from the rhizosphere of soya bean
Hui Zhao, Yue Su, Qihui Gu, Jumei Zhang, Xinqiang Xie, Qingping Wu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil
Shuang Han, Rong Tang, Shang Yang, Cheng-Jie Xie, Manik Prabhu Narsing Rao, Christopher Rensing, Guo-Hong Liu, Shun-Gui Zhou
Antonie van Leeuwenhoek.2023; 116(5): 477. CrossRef
Description of Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. isolated from the Intestines of Aegosoma sinicum Larvae
Hae-In Joe, Jee-Won Choi, June-Young Lee, Hojun Sung, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2023; 61(6): 603. CrossRef
Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae
Ju Hye Baek, Sylvia Kristyanto, Jeong Min Kim, Dong Min Han, Zhe-Xue Quan, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Muricauda myxillae sp. nov., isolated from a marine sponge (Myxilla rosacea), and reclassification of Flagellimonas hymeniacidonis as Muricauda symbiotica nom. nov.
Yea-Lin Moon, Kyung-Hyun Kim, Jin-Sook Park
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi
Jae Kyeong Lee, Ju Hye Baek, Dong Min Han, Se Hee Lee, So Young Kim, Che Ok Jeon
Journal of Microbiology and Biotechnology.2023; 33(11): 1448. CrossRef
Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
Kyeong Ryeol Kim, Jeong Min Kim, Jae Kyeong Lee, Dong Min Han, Lujiang Hao, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi
Dongwook Kim, Cameron L M Gilchrist, Jongsik Chun, Martin Steinegger
Nucleic Acids Research.2023; 51(D1): D777. CrossRef
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Carlos J Pardo-De la Hoz, Nicolas Magain, Bryan Piatkowski, Luc Cornet, Manuela Dal Forno, Ignazio Carbone, Jolanta Miadlikowska, François Lutzoni, Claudia Lemus-Solis
Systematic Biology.2023; 72(3): 694. CrossRef
Zwartia vadi sp. nov., a Novel Species of the GKS98 Cluster Isolated from a Stream, and the Reclassification of ‘Achromobacter Panacis’ as Zwartia panacis comb. nov
Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Microorganisms.2023; 11(9): 2150. CrossRef
Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks
Ying Wen, Binglin Zhang, Gaosen Zhang, Minghui Wu, Ximing Chen, Tuo Chen, Guangxiu Liu, Wei Zhang
Antonie van Leeuwenhoek.2023; 116(12): 1407. CrossRef
Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley
James T. Tambong, Renlin Xu, Maria Constanza Fleitas, Lipu Wang, Keith Hubbard, Randy Kutcher
Phytopathology®.2023; 113(11): 2091. CrossRef
Microvirga terrae sp. nov., Isolated from Soil
Kyung Hyun Kim, Ju Hye Baek, Sang Eun Jeong, Lujiang Hao, Che Ok Jeon
Current Microbiology.2023;[Epub] CrossRef
Incidence, genetic diversity, and antimicrobial resistance profiles of Vibrio parahaemolyticus in seafood in Bangkok and eastern Thailand
Chartchai Changsen, Somsak Likhitrattanapisal, Kamonwan Lunha, Wiyada Chumpol, Surasak Jiemsup, Anuphap Prachumwat, Darin Kongkasuriyachai, Supawadee Ingsriswang, Soraya Chaturongakul, Aekarin Lamalee, Suganya Yongkiettrakul, Sureemas Buates
PeerJ.2023; 11: e15283. CrossRef
Streptomonospora mangrovi sp. nov., isolated from mangrove soil showing similar metabolic capabilities, but distinct secondary metabolites profiles
Cheng Zhen, Xin-Kai Chen, Xian-Feng Ge, Wen-Zheng Liu
Archives of Microbiology.2023;[Epub] CrossRef
Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emend
Kyung Hyun Kim, Dong Min Han, Jae Kyeong Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction
Seong-In Na, Michael James Bailey, Mauricio Chalita, Jae Hyoung Cho, Jongsik Chun
Journal of Microbiology.2023; 61(7): 683. CrossRef
Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea
Kyung Hyun Kim, Jeong Min Kim, Hyun Mi Jin, Lujiang Hao, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Cutibacterium equinum sp. nov., isolated from horse faeces
Jeong Ui Yun, Hye Su Jung, Mi-Ja Jung, Hye Seon Song, Yeon Bee Kim, Yujin Kim, Joon-Gyu Kim, Seong Woon Roh, Se Hee Lee, Jun Sik Lee, Tae Woong Whon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar
José R. Morales-Poole, Clara de Vega, Kaoru Tsuji, Hans Jacquemyn, Robert R. Junker, Carlos M. Herrera, Chris Michiels, Bart Lievens, Sergio Álvarez-Pérez
Microbial Ecology.2023; 86(1): 377. CrossRef
Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden
Martina Jerabkova, Tereza Smrhova, Eglantina Lopez-Echartea, Jiri Dresler, Jachym Suman, Gabriela Kapinusova, Tomas Cajthaml, Zdena Skrob, Robin Kyclt, Jonas Fagerman, Michal Strejcek, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton
Xianfeng Ge, Shenrong Yang, Cheng Zhen, Wenzheng Liu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Phylogenomic analysis of the genus Rosenbergiella and description of Rosenbergiella gaditana sp. nov., Rosenbergiella metrosideri sp. nov., Rosenbergiella epipactidis subsp. epipactidis subsp. nov., Rosenbergiella epipactidis subsp. californiensis subsp.
Sergio Álvarez-Pérez, Clara de Vega, Kristof Vanoirbeek, Kaoru Tsuji, Hans Jacquemyn, Tadashi Fukami, Chris Michiels, Bart Lievens
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve
Shanshan Xu, Junpeng Chen, Si Chen, Qiliang Lai, Zengzhi Liu, Ying Xu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Tahibacter soli sp. nov., isolated from soil and Tahibacter amnicola sp. nov., isolated from freshwater
Ju Hye Baek, Dong Min Han, Jeong Min Kim, Baolei Jia, Ji Young Jung, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov.
Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li
Frontiers in Microbiology.2023;[Epub] CrossRef
Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil
Jie Du, Ying Zhang, Di Xin, Yuhua Xin, Jianli Zhang
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Caldimonas mangrovi sp. nov., Isolated from Mangrove Soil
S. R. Yang, Y. Y. Liu, X. F. Ge, W. Z. Liu
Microbiology.2023; 92(4): 500. CrossRef
Chitinophaga horti sp. nov., Isolated from Garden Soil
Dong Min Han, Ju Hye Baek, Dae Gyu Choi, Myeong Seo Jin, Che Ok Jeon
Current Microbiology.2023;[Epub] CrossRef
Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment
Miku Takahashi, Shoya Shinohara, Moriyuki Hamada, Tomohiko Tamura, Hideo Dohra, Shinya Kodani, Youji Nakagawa, Susumu Kokubo, Masayuki Hayakawa, Hideki Yamamura
The Journal of Antibiotics.2023; 76(2): 93. CrossRef
MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand
Nut Nithimongkolchai, Yothin Hinwan, Benjawan Kaewseekhao, Pisit Chareonsudjai, Pipat Reungsang, Ratthaphol Kraiklang, Sorujsiri Chareonsudjai, Lumyai Wonglakorn, Ploenchan Chetchotisakd, Auttawit Sirichoat, Arnone Nithichanon, Kiatichai Faksri
Infection, Genetics and Evolution.2023; 116: 105532. CrossRef
Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil
Yong-Seok Kim, Eun-Mi Hwang, Chang-Myeong Jeong, Chang-Jun Cha
Journal of Microbiology.2023; 61(10): 891. CrossRef
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Renmao Tian, Behzad Imanian
Microbiome.2023;[Epub] CrossRef
tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix
Nikolai V. Ravin, Dmitry D. Smolyakov, Nikita D. Markov, Alexey V. Beletsky, Andrey V. Mardanov, Tatyana S. Rudenko, Margarita Yu. Grabovich
Microorganisms.2023; 11(10): 2521. CrossRef
Thermomonas paludicola sp. nov., isolated from a lotus wetland
Mirae Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov., isolated from a marine red alga and emended description of the genus Octadecabacter
Myeong Seo Jin, Kyung Hyun Kim, Ju Hye Baek, Jeong Min Kim, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream
Miri S. Park, Hyeonuk Sa, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2022; 60(8): 806. CrossRef
Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey
Syariffah Nuratiqah Syed Yaacob, Fahrul Huyop, Mailin Misson, Roswanira Abdul Wahab, Nurul Huda
PeerJ.2022; 10: e13053. CrossRef
Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa)
Ai-Yun Lee, Chia-Hsuan Chen, Jong-Shian Liou, Yu-Chun Lin, Moriyuki Hamada, Yu-Ting Wang, Lin-Liang Peng, Shen-Chang Chang, Chih-Chieh Chen, Chuen-Fu Lin, Lina Huang, Chien-Hsun Huang
Life.2022; 12(11): 1749. CrossRef
Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters
Zhen-Yu Zan, Xian-Feng Ge, Rui-Rui Huang, Wen-Zheng Liu
Current Microbiology.2022;[Epub] CrossRef
Occultella gossypii sp. nov., an alkali-resistant isolate from soil sampled in a cotton field
Xianfeng Ge, Ruirui Huang, Wenzheng Liu
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment
Ju Hye Baek, Woonhee Baek, Sang Eun Jeong, Sung Chul Lee, Hyun Mi Jin, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2022; 115(3): 445. CrossRef
Amsterdam urban canals contain novel niches for methane‐cycling microorganisms
Koen A. J. Pelsma, Michiel H. in 't Zandt, Huub J. M. Op den Camp, Mike S. M. Jetten, Joshua F. Dean, Cornelia U. Welte
Environmental Microbiology.2022; 24(1): 82. CrossRef
Roseovarius carneus sp. nov., a novel bacterium isolated from a coastal phytoplankton bloom in Xiamen
Xueqiong Sun, Dan Lin, Yu Han, Jia Sun, Jianing Ye, Beihan Chen, Kai Tang
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Tenacibaculum aquimarinum sp. nov., isolated from a marine alga and seawater
Sylvia Kristyanto, Kyeong Ryeol Kim, Jaejoon Jung, Hyung Min Kim, Keunpil Kim, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Rheinheimera maricola sp. nov., isolated from seawater of the Yellow Sea
Kyung Hyun Kim, Ju Hye Baek, Ruan Wenting, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula ca
Scott A. Oliphant, Nathan S. Watson-Haigh, Krista M. Sumby, Jennifer Gardner, Scott Groom, Vladimir Jiranek
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea
Piyanat Charoenyingcharoen, Pattaraporn Yukphan, Sukunphat Malimas, Somsak Likhitrattanapisal, Somboon Tanasupawat, Yuzo Yamada
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Massilia soli sp. nov., isolated from soil
Ju Hye Baek, Woonhee Baek, Wenting Ruan, Hye Su Jung, Sung Chul Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Actinotalea soli sp. nov., isolated from Kubuqi Desert soil
Jie Du, Weiwei Ping, Ya Chen, Huancheng Pang, Pengze Bai, Siqi Cui, Jianli Zhang
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Arsenicicoccus cauae sp. nov., isolated from the blood of a pediatric gastroenteritis patient
Oh Joo Kweon, Kyung Hyun Kim, Hyung Min Kim, Shehzad Abid Khan, Ji Hun Jeong, Yong Kwan Lim, Hye Ryoun Kim, Che Ok Jeon, Mi-Kyung Lee
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., Isolated from Soil
Shehzad Abid Khan, Hyung Min Kim, Ju Hye Baek, Hye Su Jung, Che Ok Jeon
Journal of Microbiology and Biotechnology.2021; 31(9): 1210. CrossRef
Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea
Hyung Min Kim, Dong Min Han, Byung Hee Chun, Hye Su Jung, Kyung Hyun Kim, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Effects of multi-species probiotic supplementation on alcohol metabolism in rats: Tae-Joong Lim , Sanghyun Lim , Jong Hyun Yoon , Myung Jun Chung; J. Microbiol. 2021;59(4):417-425. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0573-2

539 View
1 Download
11 Web of Science
12 Crossref

Abstract PDF

Probiotics are known to protect against liver damage induced by the alcohol and acetaldehyde accumulation associated with alcohol intake. However, there have been few studies of the direct effect of probiotics on alcohol metabolism, and the types of probiotics that were previously analyzed were few in number. Here, we investigated the effects of 19 probiotic species on alcohol and acetaldehyde metabolism. Four probiotic species that had a relatively high tolerance to alcohol and metabolized alcohol and acetaldehyde effectively were identified: Lactobacillus gasseri CBT LGA1, Lactobacillus casei CBT LC5, Bifidobacterium lactis CBT BL3, and Bifidobacterium breve CBT BR3. These species also demonstrated high mRNA expression of alcohol and acetaldehyde dehydrogenases. Pro- AP4, a mixture of these four probiotics species and excipient, was then administered to rats for 2 weeks in advance of acute alcohol administration. The serum alcohol and acetaldehyde concentrations were significantly lower in the ProAP4-administered group than in the control and excipient groups. Thus, the administration of ProAP4, containing four probiotic species, quickly lowers blood alcohol and acetaldehyde concentrations in an alcohol and acetaldehyde dehydrogenasedependent manner. Furthermore, the serum alanine aminotransferase activity, which is indicative of liver damage, was significantly lower in the ProAP4 group than in the control group. The present findings suggest that ProAP4 may be an effective means of limiting alcohol-induced liver damage.

Citations

Citations to this article as recorded by

Degradation effects and mechanisms of Limosilactobacillus fermentum on ethanol
Lingling Zhang, Yuhong Zhang, Shijian Liu, Jiajia Song, Huayi Suo
Food & Function.2024; 15(20): 10283. CrossRef
Reduction of Insulin Resistance by Momordica Charantia with Lactobacillus Acidophilus CBT-LA1 or Lactiplantibacillus Plantarum CBT-LP3 Improves Hepatosteatosis
Dong-Jin Kim, Ju Sung Lee, Seungwoo Kim, Sang Kyun Park, Yeo-Sang Yoon, Yougku Ryu, Myung Jun Chung
Microbiology and Biotechnology Letters.2024; 52(3): 275. CrossRef
Investigation of volatile compounds during fermentation of Elaeagnus moorcroftii Wall.ex schlecht. juice by Bifidobacterium animalis subsp. lactis HN-3 and Lacticaseibacillus paracasei YL-29
Yixuan Wang, Wenhao Li, Xiaojun Wang, Qi Hu, Junkai Kong, Xiu wang, Zhenghui Lan, Chenxi Wang, Yan Zhang
Food Chemistry: X.2024; 21: 101171. CrossRef
Gut microbiome in alcohol use disorder: Implications for health outcomes and therapeutic strategies-a literature review
Ilias Koutromanos, Evangelia Legaki, Maria Gazouli, Efthimios Vasilopoulos, Anastasios Kouzoupis, Elias Tzavellas
World Journal of Methodology.2024;[Epub] CrossRef
Oral Administration of Bifidobacterium lactis Ameliorates Cognitive Deficits in Mice Intracerebroventricularly Administered Amyloid Beta via Regulation the Activation of Mitogen-activated Protein Kinases
Jong Kyu Choi, Oh Yun Kwon, Seung Ho Lee
Food Science of Animal Resources.2024; 44(3): 607. CrossRef
Gut microbiome diversity, variability, and latent community types compared with shifts in body weight during the freshman year of college in dormitory-housed adolescents
Alex E. Mohr, Mary M. Ahern, Dorothy D. Sears, Meg Bruening, Corrie M. Whisner
Gut Microbes.2023;[Epub] CrossRef
A Synbiotic Ameliorates Con A‐Induced Autoimmune Hepatitis in Mice through Modulation of Gut Microbiota and Immune Imbalance
Qingqing Liu, Hao Yang, Xing Kang, Haixia Tian, Yongbo Kang, Lin Li, Xiaodan Yang, Haixia Liu, Peng Ren, Xiaoyu Kuang, Mingwei Tong, Weiping Fan
Molecular Nutrition & Food Research.2023;[Epub] CrossRef
Probiotic cheese improves alcohol metabolism and alleviates alcohol-induced liver injury via the SIRT1/AMPK signaling pathway
Jong-Hwa Kim, Dohyun Woo, YoHan Nam, Jihye Baek, Ji-Yeon Lee, Wonyong Kim
Journal of Functional Foods.2023; 108: 105736. CrossRef
Harnessing the potential of probiotics in the treatment of alcoholic liver disorders
Garima Mishra, Pradeep Singh, Mulugeta Molla, Yohannes Shumet Yimer, Subas Chandra Dinda, Phool Chandra, Bhuvnesh Kumar Singh, Samuel Berihun Dagnew, Abraham Nigussie Assefa, Amien Ewunetie
Frontiers in Pharmacology.2023;[Epub] CrossRef
Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases
Jiajun Yang, Shunyi Qin, Hao Zhang
Frontiers in Immunology.2022;[Epub] CrossRef
Lactobacillus rhamnosus CBT-LR5 Improves Lipid Metabolism by Enhancing Vitamin Absorption
Dong-Jin Kim, Tai Yeub Kim, Yeo-Sang Yoon, Yongku Ryu, Myung Jun Chung
Microbiology and Biotechnology Letters.2022; 50(4): 477. CrossRef
Regulation of Alcohol and Acetaldehyde Metabolism by a Mixture of Lactobacillus and Bifidobacterium Species in Human
Su-Jin Jung, Ji-Hyun Hwang, Eun-Ock Park, Seung-Ok Lee, Yun-Jo Chung, Myung-Jun Chung, Sanghyun Lim, Tae-Joong Lim, Yunhi Ha, Byung-Hyun Park, Soo-Wan Chae
Nutrients.2021; 13(6): 1875. CrossRef

Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing: Hyojung Kim , Sora Kim , Sungwon Jung; J. Microbiol. 2020;58(3):193-205. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9556-y

359 View
0 Download
28 Web of Science
30 Crossref

Abstract PDF

Recent studies on microbiome highlighted their importance in various environments including human, where they are involved in multiple biological contexts such as immune mechanism, drug response, and metabolism. The rapid increase of new findings in microbiome research is partly due to the technological advances in microbiome identification, including the next-generation sequencing technologies. Several applications of different next-generation sequencing platforms exist for microbiome identification, but the most popular method is using short-read sequencing technology to profile targeted regions of 16S rRNA genes of microbiome because of its low-cost and generally reliable performance of identifying overall microbiome compositions. The analysis of targeted 16S rRNA sequencing data requires multiple steps of data processing and systematic analysis, and many software tools have been proposed for such procedures. However, properly organizing and using such software tools still require certain level of expertise with computational environments. The purpose of this article is introducing the concept of computational analysis of 16S rRNA sequencing data to microbiologists and providing easy-to-follow and step-by-step instructions of using recent software tools of microbiome analysis. This instruction may be used as a quick guideline for general next-generation sequencing-based microbiome studies or a template of constructing own software pipelines for customized analysis.

Citations

Citations to this article as recorded by

PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts
Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin
npj Biofilms and Microbiomes.2025;[Epub] CrossRef
Increased bacterial load of Filifactor alocis in deep periodontal pockets discriminate between periodontitis stage 3 and 4
Reem H. Faisal, Alaa O. Ali
Frontiers in Oral Health.2025;[Epub] CrossRef
Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake
Rongbing Guo, Yuguang Chang, Dandan Wang, Hanxue Sun, Tiantian Gu, Yibo Zong, Shiheng Zhou, Zhizhou Huang, Li Chen, Yong Tian, Wenwu Xu, Lizhi Lu, Tao Zeng
Animal Microbiome.2025;[Epub] CrossRef
Understanding the implicit effects of 16S rRNA gene databases on microbial bioindicator studies
Vitória da Silva Pereira Domingues, Lucy Seldin, Diogo Jurelevicius
Aquatic Toxicology.2025; 283: 107351. CrossRef
Cyber-Biosecurity Challenges in Next-Generation Sequencing: A Comprehensive Analysis of Emerging Threat Vectors
Nasreen Anjum, Hani Alshahrani, Asadullah Shaikh, Mahreen-Ul-Hassan, Mehreen Kiran, Shah Raz, Abu Alam
IEEE Access.2025; 13: 52006. CrossRef
Pathogenic factors of Filifactor alocis and Streptococcus gordonii identified in patients with inflammatory periodontal diseases
I. A. Gimranova, A. H. Baymiev, G. M. Akmalova, V. A. Gritsenko
Parodontologiya.2025;[Epub] CrossRef
Role of Acupuncture on Gut Microbiome Modulation: A Systematic Review of Randomized Controlled Trials
Venkatalakshmi Saravanan, A Mooventhan, E Dharani, Sathiyavathi Gopi, N Mangaiarkarasi
Acupuncture & Electro-Therapeutics Research: International Journal of Integrated Medicine.2025; 49(4): 275. CrossRef
Microbial Population Analysis Based on 16S rRNA Detection and Its Application in Epidemic Disease Warning
逸欣王
Advances in Microbiology.2024; 13(03): 216. CrossRef
The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing
Nabeel Merali, Tarak Chouari, Casie Sweeney, James Halle-Smith, Maria-Danae Jessel, Bing Wang, James O’ Brien, Satoshi Suyama, José I. Jiménez, Keith J. Roberts, Eirini Velliou, Shivan Sivakumar, Timothy A. Rockall, Ayse Demirkan, Virginia Pedicord, Dongm
International Journal of Surgery.2024; 110(10): 6771. CrossRef
Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered Fish Totoaba macdonaldi
Itzel Soledad Pérez-Bustamante, Roberto Cruz-Flores, Jesús Antonio López-Carvallo, Samuel Sánchez-Serrano
Microorganisms.2024; 12(11): 2119. CrossRef
The Synergistic Impact of a Novel Plant Growth-Promoting Rhizobacterial Consortium and Ascophyllum nodosum Seaweed Extract on Rhizosphere Microbiome Dynamics and Growth Enhancement in Oryza sativa L. RD79
Pisit Thamvithayakorn, Cherdchai Phosri, Louisa Robinson-Boyer, Puenisara Limnonthakul, John H. Doonan, Nuttika Suwannasai
Agronomy.2024; 14(11): 2698. CrossRef
Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome
Hamidreza Taherkhani, Azadeh KavianFar, Sargol Aminnezhad, Hossein Lanjanian, Ali Ahmadi, Sadegh Azimzadeh, Ali Masoudi-Nejad
Heliyon.2024; 10(4): e24775. CrossRef
Patent Mining on the Use of Antioxidant Phytochemicals in the Technological Development for the Prevention and Treatment of Periodontitis
Paulo José Lima Juiz, Luiza Teles Barbalho Ferreira, Edilson Araújo Pires, Cristiane Flora Villarreal
Antioxidants.2024; 13(5): 566. CrossRef
Periodontal Hastalıklar: Başlıca Risk Faktörleri
Tuba USTAOĞLU, Deniz MIHÇIOĞLU
Cumhuriyet Üniversitesi Sağlık Bilimleri Enstitüsü Dergisi.2023; 8(3): 501. CrossRef
Potential effects of gut microbiota on host cancers: focus on immunity, DNA damage, cellular pathways, and anticancer therapy
Jiaao Sun, Feng Chen, Guangzhen Wu
The ISME Journal.2023; 17(10): 1535. CrossRef
Using microbiome information to understand and improve animal performance
Jeferson Menezes Lourenco, Christina Breanne Welch
Italian Journal of Animal Science.2022; 21(1): 899. CrossRef
The Influence of Periodontal Disease on Oral Health Quality of Life in Patients with Cardiovascular Disease: A Cross-Sectional Observational Single-Center Study
Pompilia Camelia Lazureanu, Florina Georgeta Popescu, Laura Stef, Mircea Focsa, Monica Adriana Vaida, Romeo Mihaila
Medicina.2022; 58(5): 584. CrossRef
Osteoimmunology in Periodontitis: Local Proteins and Compounds to Alleviate Periodontitis
Kridtapat Sirisereephap, Tomoki Maekawa, Hikaru Tamura, Takumi Hiyoshi, Hisanori Domon, Toshihito Isono, Yutaka Terao, Takeyasu Maeda, Koichi Tabeta
International Journal of Molecular Sciences.2022; 23(10): 5540. CrossRef
Effects of oral health intervention strategies on cognition and microbiota alterations in patients with mild Alzheimer's disease: A randomized controlled trial
Lili Chen, Huizhen Cao, Xiaoqi Wu, Xinhua Xu, Xinli Ji, Bixia Wang, Ping Zhang, Hong Li
Geriatric Nursing.2022; 48: 103. CrossRef
Lung microbiome in children with hematological malignancies and lower respiratory tract infections
Yun Zhang, Haonan Ning, Wenyu Zheng, Jing Liu, Fuhai Li, Junfei Chen
Frontiers in Oncology.2022;[Epub] CrossRef
Defining the baseline of pulmonary microbiota in healthy populations and influencing factors
Zhuoning Tang, Sen Yang, Zilong He
Highlights in Science, Engineering and Technology.2022; 11: 38. CrossRef
Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo
BMC Bioinformatics.2022;[Epub] CrossRef
Periodontal Disease: The Good, The Bad, and The Unknown
Lea M. Sedghi, Margot Bacino, Yvonne Lorraine Kapila
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
Microbiome-immune interactions in tuberculosis
Giorgia Mori, Mark Morrison, Antje Blumenthal, N.Luisa Hiller
PLOS Pathogens.2021; 17(4): e1009377. CrossRef
Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets
Lauren E. Eldred, R. Greg Thorn, David Roy Smith
Frontiers in Genetics.2021;[Epub] CrossRef
Xylanase impact beyond performance: A microbiome approach in laying hens
Veerle Van Hoeck, Ingrid Somers, Anas Abdelqader, Alexandra L. Wealleans, Sandy Van de Craen, Dany Morisset, Arda Yildirim
PLOS ONE.2021; 16(9): e0257681. CrossRef
User guides for biologists to learn computational methods
Dokyun Na
Journal of Microbiology.2020; 58(3): 173. CrossRef
High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(11): 893. CrossRef
Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range
Janet L. H. Sperling, Daniel Fitzgerald, Felix A. H. Sperling, Katharine E. Magor
Tropical Medicine and Infectious Disease.2020; 5(4): 173. CrossRef

Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(12):1048-1055. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9260-y

268 View
0 Download
3 Web of Science
4 Crossref

Abstract PDF

A Gram-stain-negative, strictly aerobic, marine bacterium, designated GH2-2T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) in Gangwha Island, the Republic of Korea. The cells of the organism were oxidase- positive, catalase-positive, flagellated, short rods that grew at 10–40°C, pH 4–10, and 0–13% (w/v) NaCl. The predominant ubiquinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The major fatty acid is C18:1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed an independent lineage at the base of the radiation encompassing members of the genus Thioclava, except for Thioclava arenosa. The closest relatives were T. nitratireducens (96.03% sequence similarity) and T. dalianensis (95.97%). The genome size and DNA G+C content were 3.77 Mbp and 59.6 mol%, respectively. Phylogenomic analysis supported phylogenetic distinctness based on 16S rRNA gene sequences. Average nucleotide identity values were 73.6–74.0% between the novel strain and members of the genus Thioclava. On the basis of data obtained from a polyphasic approach, the strain GH2-2T (= KCTC 62124T = DSM 105743T) represents a novel species of a new genus for which the name Hahyoungchilella caricis gen. nov., sp. nov. is proposed. Moreover, the transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava gen. nov. as Pseudothioclava arenosa comb. nov. is also proposed. Finally, Thioclava electrotropha Chang et al. 2018 is proposed to be a later heterosynonym of Thioclava sediminum Liu et al. 2017.

Citations

Citations to this article as recorded by

Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat
Zhaobin Huang, Meiqin Li, Aharon Oren, Qiliang Lai
Frontiers in Microbiology.2024;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef

Martelella lutilitoris sp. nov., isolated from a tidal mudflat: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(11):976-981. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9259-4

280 View
0 Download
6 Web of Science
8 Crossref

Abstract PDF

A novel, Gram-stain-negative, marine bacterium, designated GH2-6T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) collected in Gangwha Island, the Republic of Korea. The cells of the organism were strictly aerobic, oxidase- and catalase-positive, non-flagellated rods. Growth occurred at 20–45°C, pH 5–10, and 0.5–9 (w/v) NaCl. The requirement of Na+ for growth (0.5–3%) was observed. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and a glycolipid. The predominant fatty acids were C18:1 ω7c, C18:0, C16:0, C19:0 cyclo ω8c, C18:1 ω7c 11-methyl and summed feature 2 (C14:0 3-OH and/or C16:1 iso I). The genome size was 4.45 Mb and the G+C content of the genomic DNA was 61.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH2-6T belonged to genus Martelella and formed a tight cluster with M. radicis BM5-7T and M. endophytica YC6887T. Levels of 16S rRNA gene sequence similarity between the novel isolate and members of the genus were 99.3–95.5%, but strain GH2-6T possessed an extended loop (49 nucleotides in length) between positions 187 and 213 of the 16S rRNA gene sequence (E. coli numbering). DDH values in vitro between the novel isolate and the closest relatives were 23.2±12.8 – 46.3±5.2%. On the basis of polyphasic data presented in this study, the type strain GH2-6T (= KACC 19403T = KCTC 62125T = NBRC 113212T) represents a novel species of the genus Martelella for which the name Martelella lutilitoris sp. nov. is proposed.

Citations

Citations to this article as recorded by

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20
Jung-Yun Lee, Dong-Hun Kim
Journal of Microbiology and Biotechnology.2022; 32(11): 1427. CrossRef
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf
Mi Li, Chenghai Gao, Yuyao Feng, Kai Liu, Pei Cao, Yonghong Liu, Xiangxi Yi
Archives of Microbiology.2021; 203(4): 1779. CrossRef
Insights from comparative proteomic analysis into degradation of phenanthrene and salt tolerance by the halophilic Martelella strain AD-3
Xin Chen, Weiwei Wang, Haiyang Hu, Hongzhi Tang, Yongdi Liu, Ping Xu, Kuangfei Lin, Changzheng Cui
Ecotoxicology.2021; 30(7): 1499. CrossRef
Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas
Dabin Jeon, In Seop Kim, Hanna Choe, Ji-Sun Kim, Soon Dong Lee
Archives of Microbiology.2021; 203(6): 2843. CrossRef
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment
Jung-Yun Lee, Dong-Hun Lee, Dong-Hun Kim
Microorganisms.2021; 9(8): 1736. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef
Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of
Young-Ju Kim, Soon Dong Lee
Journal of Microbiology.2019; 57(12): 1048. CrossRef

Comparative portrayal of ocular surface microbe with and without dry eye: ZhenHao Li , Yufang Gong , ShuZe Chen , SiQi Li , Yu Zhang , HuiMin Zhong , ZhouCheng Wang , YiFan Chen , QiXin Deng , YuTing Jiang , LiYing Li , Min Fu , GuoGuo Yi; J. Microbiol. 2019;57(11):1025-1032. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9127-2

377 View
0 Download
56 Web of Science
63 Crossref

Abstract PDF

To compare the ocular surface (OS) microbial communities and diversity between dry eye (DE) and non-DE (NDE). Furthermore, we compared meibomian gland dysfunction (MGD) and non-MGD (NMGD) among DE subjects. The V3-V4 region of 16S rRNA gene high-throughput sequencing was performed in the conjunctival swab samples to investigate the composition of the OS bacterial community in DE (n=35) and NDE (n=54) and compared the composition of MGD (n=25) and NMGD (n=10) among DE subjects. Deep sequencing of OS 16S rDNA from DE (n=35) and NDE (n=54) demonstrated great a difference in alpha and beta diversity between the OS bacterial flora (P < 0.05). The similar OS microbial structures were shown at the phylum and genus levels by bioinformatics analysis between them, and in LEfSe (linear discriminant analysis effect size) analysis, Bacteroidia and Bacteroidetes were enriched in DE, while Pseudomonas was plentiful in NDE (linear discriminant analysis [LDA] > 4.0). Among the DE group, there was no significant difference in α and β diversity between MGD and NMGD (P > 0.05). Surprisingly, Bacilli was the dominant microbe in MGD, and Bacteroidetes was the superior bacteria in NMGD among DE subjects (LDA > 4.0). Different diversity of OS bacteria composition between DE and NDE and the altered diversity of OS bacteria may play an important role in DE. Moreover, the lower dominance of OS bacteria in DE may be associated with the occurrence and development of DE. Although there was no significant difference in alpha and beta analysis, the OS dominant microbe between MGD and NMGD among DE was different.

Citations

Citations to this article as recorded by

Potential Risks of Ocular Molecular and Cellular Changes in Spaceflight
Ryung Lee, Joshua Ong, Ethan Waisberg, Thomas Mader, John Berdahl, Alex Suh, Nicholas Panzo, Hamza Memon, Ritu Sampige, Blake Katsev, Cihan Mehmet Kadipasaoglu, Christopher E. Mason, Afshin Beheshti, Sara R. Zwart, Scott M. Smith, Andrew G. Lee
Seminars in Ophthalmology.2025; : 1. CrossRef
Microbial Interconnections in One Health: A Critical Nexus Between Companion Animals and Human Microbiomes
Stylianos Skoufos, Elisavet Stavropoulou, Christina Tsigalou, Chrysoula (Chrysa) Voidarou
Microorganisms.2025; 13(7): 1564. CrossRef
From Dysbiosis to Disease: The Microbiome’s Influence on Uveitis Pathogenesis
Priya D. Samalia, Jahnvee Solanki, Joseph Kam, Lize Angelo, Rachael L. Niederer
Microorganisms.2025; 13(2): 271. CrossRef
Characterization of Vitreous Microbiota Dysbiosis Associated with Proliferative Diabetic Retinopathy
Fangying Song, Yan Qi, Wenhui Ma, Jun Li, Yan Gao, Xiubin Ma
Diabetes, Metabolic Syndrome and Obesity.2025; Volume 18: 2451. CrossRef
Analysis of Ocular Surface Microbiota Composition and Influencing Factors Based on 16S rRNA Gene Sequencing
昭宇陈
Advances in Clinical Medicine.2025; 15(06): 283. CrossRef
Alterations of ocular surface microbiome in glaucoma and its association with dry eye
Houyem Kamdougha, Bernard Taminiau, Papa Abdoulaye Fall, Saloua Ben Amor, Amira Trigui, Georges Daube, Basma Mnif
Journal of Medical Microbiology .2025;[Epub] CrossRef
Best practices for the experimental design of one health studies on companion animal and owner microbiomes – From data collection to analysis
Suzanne B. Clougher, Dagmara Niedziela, Piera Versura, Grace Mulcahy
One Health.2025; 20: 100977. CrossRef
What is the impact of microbiota on dry eye: a literature review of the gut-eye axis
Jiaping Song, He Dong, Tingting Wang, He Yu, Jian Yu, Shaokang Ma, Xiaohai Song, Qianhui Sun, Yongcheng Xu, Mingkai Liu
BMC Ophthalmology.2024;[Epub] CrossRef
Axis "microbiota – gut – eye": a review
Irina N. Zakharova, Irina V. Berezhnaya, Diana K. Dmitrieva, Viktoria V. Pupykina
Pediatrics. Consilium Medicum.2024; (2): 179. CrossRef
Effects of dietary imbalances of micro- and macronutrients on the ocular microbiome and its implications in dry eye disease
Madeline Pilkington, Declan Lloyd, Brad Guo, Stephanie L. Watson, Kenneth Gek-Jin Ooi
Exploration of Medicine.2024; : 127. CrossRef
Unique composition of ocular surface microbiome in the old patients with dry eye and diabetes mellitus in a community from Shanghai, China
Zhangling Chen, Senlin Lin, Yi Xu, Lina Lu, Haidong Zou
BMC Microbiology.2024;[Epub] CrossRef
The Ocular Microbiome: Micro-Steps Towards Macro-Shift in Targeted Treatment? A Comprehensive Review
Ewelina Trojacka, Justyna Izdebska, Jacek Szaflik, J. Przybek-Skrzypecka
Microorganisms.2024; 12(11): 2232. CrossRef
Ocular microbiota types and longitudinal microbiota alterations in patients with chronic dacryocystitis with and without antibiotic pretreatment
Shengru Wu, Limin Zhu, Tingting Wang, Chenguang Zhang, Jiaqi Lin, Yanjin He, Junhu Yao, Tingting Lin, Juan Du
iMetaOmics.2024;[Epub] CrossRef
Review on the Treatment of Dry Eye Based on Intestinal Axial Theory
伟琴王
Advances in Clinical Medicine.2024; 14(11): 152. CrossRef
Longitudinal Changes of Ocular Surface Microbiome in Patients Undergoing Hemopoietic Stem Cell Transplant (HSCT)
Suzanne Clougher, Marco Severgnini, Antonella Marangoni, Clarissa Consolandi, Tania Camboni, Sara Morselli, Mario Arpinati, Francesca Bonifazi, Michele Dicataldo, Tiziana Lazzarotto, Luigi Fontana, Piera Versura
Journal of Clinical Medicine.2023; 13(1): 208. CrossRef
Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
Kang Xiao, Zhengyu Chen, Qin Long
Journal of Microbiology.2023; 61(5): 571. CrossRef
Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye
Zhangling Chen, Ying Xiao, Yan Jia, Qiurong Lin, Yu Qian, Lipu Cui, Zhaoyu Xiang, Mingfang Li, Chenhao Yang, Haidong Zou
BMC Microbiology.2023;[Epub] CrossRef
Contact lenses and ocular dysbiosis, from the transitory to the pathological
B. Barrera, A. Bustamante, M. Marín-Cornuy, P. Aguila-Torres
Archivos de la Sociedad Española de Oftalmología (English Edition).2023; 98(10): 586. CrossRef
Investigating the Ocular Surface Microbiome: What Can It Tell Us?
Virginie G Peter, Sophia C Morandi, Elio L Herzog, Martin S Zinkernagel, Denise C Zysset-Burri
Clinical Ophthalmology.2023; Volume 17: 259. CrossRef
Tear film microbiome in Sjogren’s and non-Sjogren’s aqueous deficiency dry eye
Spandita Pal, Gorati Vani, Pragnya Rao Donthineni, Sayan Basu, Kotakonda Arunasri
Indian Journal of Ophthalmology.2023; 71(4): 1566. CrossRef
Lentes de contacto y disbiosis ocular, de lo transitorio a lo patológico
B. Barrera, A. Bustamante, M. Marín-Cornuy, P. Aguila-Torres
Archivos de la Sociedad Española de Oftalmología.2023; 98(10): 586. CrossRef
Targeting the Gut–Eye Axis: An Emerging Strategy to Face Ocular Diseases
Lucrezia Irene Maria Campagnoli, Angelica Varesi, Annalisa Barbieri, Nicoletta Marchesi, Alessia Pascale
International Journal of Molecular Sciences.2023; 24(17): 13338. CrossRef
Challenges and insights in the exploration of the low abundance human ocular surface microbiome
Elio L. Herzog, Marco Kreuzer, Martin S. Zinkernagel, Denise C. Zysset-Burri
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef
Ocular surface microbiota dysbiosis contributes to the high prevalence of dry eye disease in diabetic patients
Qingyu An, Haidong Zou
Critical Reviews in Microbiology.2023; 49(6): 805. CrossRef
Meibomian Gland Dysfunction Clinical Practice Guidelines
Shiro Amano, Jun Shimazaki, Norihiko Yokoi, Yuichi Hori, Reiko Arita, Hiroto Obata, Motoko Kawashima, Shizuka Koh, Takashi Suzuki, Tomo Suzuki, Masahiko Yamaguchi, Masakazu Yamada, Takashi Itokawa, Hiroko Iwashita, Tomohiko Usui, Miki Uchino, Fumika Oya,
Japanese Journal of Ophthalmology.2023; 67(4): 448. CrossRef
Effects of Carboxymethylcellulose Artificial Tears on Ocular Surface Microbiome Diversity and Composition, A Randomized Controlled Trial
Yujia Zhou, Gurjit S. Sidhu, Joan A. Whitlock, Bishoy Abdelmalik, Zachary Mayer, Youlei Li, Gary P. Wang, Walter A. Steigleman
Translational Vision Science & Technology.2023; 12(8): 5. CrossRef
Impact of Exposomes on Ocular Surface Diseases
Merrelynn Hong, Louis Tong, Jodhbir S. Mehta, Hon Shing Ong
International Journal of Molecular Sciences.2023; 24(14): 11273. CrossRef
The Microbiome, Ocular Surface, and Corneal Disorders
Michael J. Zilliox, Charles S. Bouchard
The American Journal of Pathology.2023; 193(11): 1648. CrossRef
Ocular microbiome changes in dry eye disease and meibomian gland dysfunction
Jerome Ozkan, Marwan E. Majzoub, Minas Coroneo, Torsten Thomas, Mark Willcox
Experimental Eye Research.2023; 235: 109615. CrossRef
An insight on the eye bacterial microbiota and its role on dry eye disease
Joicye Hernández‐Zulueta, José Navarro‐Partida, Oscar Eduardo Sánchez‐Aguilar, Héctor Daniel Santa Cruz‐Pavlovich, Carlos Rodrigo Castro‐Castañeda, Alejandro González‐De la Rosa
APMIS.2023; 131(3): 103. CrossRef
Ocular conjunctival microbiome profiling in dry eye disease: A case control pilot study
Noopur Gupta, Jyoti Chhibber-Goel, Yogita Gupta, Souvik Mukherjee, Arindam Maitra, Amit Sharma, Radhika Tandon
Indian Journal of Ophthalmology.2023; 71(4): 1574. CrossRef
Significantly different results in the ocular surface microbiome detected by tear paper and conjunctival swab
Zhangling Chen, Zhaoyu Xiang, Lipu Cui, Xinran Qin, Shuli Chen, Huiyi Jin, Haidong Zou
BMC Microbiology.2023;[Epub] CrossRef
DNA extraction protocol impacts ocular surface microbiome profile
Heleen Delbeke, Ingele Casteels, Marie Joossens
Frontiers in Microbiology.2023;[Epub] CrossRef
Composition and diversity of meibum microbiota in meibomian gland dysfunction and the correlation with tear cytokine levels
Ubonwan Rasaruck, Ngamjit Kasetsuwan, Thanachaporn Kittipibul, Pisut Pongchaikul, Tanittha Chatsuwan, Kofi Asiedu
PLOS ONE.2023; 18(12): e0296296. CrossRef
Visualization of normal ocular surface microflora via impression cytology sample using scanning electron microscopy with lanthanide contrasting
M.V. Kravchik, E.S. Rodina, A.M. Subbot, O.I. Pimonova, E.I. Fettser, I.A. Novikov
Vestnik oftal'mologii.2022; 138(6): 5. CrossRef
The species-level microbiota of healthy eyes revealed by the integration of metataxonomics with culturomics and genome analysis
Kui Dong, Ji Pu, Jing Yang, Guohong Zhou, Xuan Ji, Zhiming Kang, Juan Li, Min Yuan, Xiaoling Ning, Zhaoxia Zhang, XingYu Ma, Yanpeng Cheng, Hong Li, Qin Ma, Hong Li, Lijun Zhao, Wenjing Lei, Bin Sun, Jianguo Xu
Frontiers in Microbiology.2022;[Epub] CrossRef
Metagenomic profiling of ocular surface microbiome changes in Demodex blepharitis patients
Yana Fu, Jie Wu, Dandan Wang, Tiankun Li, Xinwei Shi, Lu Li, Minying Zhu, Zuhui Zhang, Xinxin Yu, Qi Dai
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Comparison of the ocular surface microbiota between thyroid-associated ophthalmopathy patients and healthy subjects
Xuan Ji, Kui Dong, Ji Pu, Jing Yang, Zhaoxia Zhang, Xiaoling Ning, Qin Ma, Zhiming Kang, Jianguo Xu, Bin Sun
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Microbiological Characteristics of Ocular Surface Associated With Dry Eye in Children and Adolescents With Diabetes Mellitus
Zhangling Chen, Yan Jia, Ying Xiao, Qiurong Lin, Yu Qian, Zhaoyu Xiang, Lipu Cui, Xinran Qin, Shuli Chen, Chenhao Yang, Haidong Zou
Investigative Opthalmology & Visual Science.2022; 63(13): 20. CrossRef
Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome
Hang Song, Kang Xiao, Zhengyu Chen, Qin Long
Frontiers in Medicine.2022;[Epub] CrossRef
Bacteria and Dry Eye: A Narrative Review
Yuchen Wang, Yi Ding, Xiaodan Jiang, Jiarui Yang, Xuemin Li
Journal of Clinical Medicine.2022; 11(14): 4019. CrossRef
Eye Make-up Products and Dry Eye Disease: A Mini Review
Mazyar Yazdani, Katja Benedikte Prestø Elgstøen, Tor Paaske Utheim
Current Eye Research.2022; 47(1): 1. CrossRef
The Role of the Ocular Surface Microbiome (OSM) in Diseases of the Anterior Segment and Ocular Surface
Kara M. Cavuoto, Angela Y. Zhu
Current Ophthalmology Reports.2022; 10(4): 179. CrossRef
Effects of Sodium Hyaluronate Eye Drops With or Without Preservatives on Ocular Surface Bacterial Microbiota
Yanlin Zhong, Xie Fang, Xuemei Wang, Yu-An Lin, Huping Wu, Cheng Li
Frontiers in Medicine.2022;[Epub] CrossRef
Ocular surface microbiota: Ophthalmic infectious disease and probiotics
Ming-Cheng Chiang, Edward Chern
Frontiers in Microbiology.2022;[Epub] CrossRef
The Effect of Topical Anesthetics on 16S Ribosomal Ribonucleic Acid Amplicon Sequencing Results in Ocular Surface Microbiome Research
Heleen Delbeke, Ingele Casteels, Marie Joossens
Translational Vision Science & Technology.2022; 11(3): 2. CrossRef
Shotgun metagenomic sequencing analysis of ocular surface microbiome in Singapore residents with mild dry eye
Louis Tong, Florentin Constancias, Aihua Hou, Song Lin Chua, Daniela I. Drautz-Moses, Stephan Christoph Schuster, Liang Yang, Rohan B. H. Williams, Staffan Kjelleberg
Frontiers in Medicine.2022;[Epub] CrossRef
Characterization of Conjunctival Sac Microbiome from Patients with Allergic Conjunctivitis
Hang Song, Kang Xiao, Hanyi Min, Zhengyu Chen, Qin Long
Journal of Clinical Medicine.2022; 11(4): 1130. CrossRef
Neutrophil Extracellular Traps (NETs) in Ocular Diseases: An Update
Jia Zeng, Min Wu, Yamei Zhou, Manhui Zhu, Xiaojuan Liu
Biomolecules.2022; 12(10): 1440. CrossRef
Temporal impacts of topical ceftazidime and tobramycin-vancomycin mixtures on the ocular surface microbiota in rabbits
Ran Xue, Qinghua Liu, Jingwei Li, Jinliang Jiang, Yan Zong, Xiuping Liu, Kaili Wu
Experimental Eye Research.2022; 220: 109098. CrossRef
Updates in diagnostics, treatments, and correlations between oral and ocular manifestations of Sjogren's syndrome
Hassaam S. Choudhry, Shayan Hosseini, Hannaan S. Choudhry, Mahnaz Fatahzadeh, Reena Khianey, Mohammad H. Dastjerdi
The Ocular Surface.2022; 26: 75. CrossRef
Ocular Surface Microbiota in Contact Lens Users and Contact-Lens-Associated Bacterial Keratitis
Jasmine Andersson, Josef K. Vogt, Marlene D. Dalgaard, Oluf Pedersen, Kim Holmgaard, Steffen Heegaard
Vision.2021; 5(2): 27. CrossRef
Ocular surface response of two preservative-free cylcosporine A emulsion eye drops in a mouse model of dry eye
Philippe Daull, Takashi Nagano, Emilie Gros, Laurence Feraille, Stefano Barabino, Jean-Sébastien Garrigue
Current Eye Research.2021; 46(8): 1096. CrossRef
Comparison of the Ocular Microbiomes of Dry Eye Patients With and Without Autoimmune Disease
Yun Qi, Yong Wan, Tianhui Li, Ming Zhang, Yu Song, Yaguang Hu, Yining Sun, Li Li
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Ocular surface microbiota in patients with aqueous tear-deficient dry eye
Jasmine Andersson, Josef K. Vogt, Marlene D. Dalgaard, Oluf Pedersen, Kim Holmgaard, Steffen Heegaard
The Ocular Surface.2021; 19: 210. CrossRef
Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data
Heleen Delbeke, Saif Younas, Ingele Casteels, Marie Joossens
Acta Ophthalmologica.2021; 99(1): 16. CrossRef
Ocular Surface Microbiota in Diabetic Patients With Dry Eye Disease
Zhang Zhang, Xinrong Zou, Wenwen Xue, Pei Zhang, Shanshan Wang, Haidong Zou
Investigative Opthalmology & Visual Science.2021; 62(12): 13. CrossRef
Demodex Infection Changes Ocular Surface Microbial Communities, in Which Meibomian Gland Dysfunction May Play a Role
Xiaotian Liang, Yingli Li, Ke Xiong, Shuze Chen, Zhenhao Li, Zhihan Zhang, Zhaoxia Xia, Guoguo Yi, Min Fu
Ophthalmology and Therapy.2021; 10(3): 601. CrossRef
The ocular surface immune system through the eyes of aging
Jeremias G. Galletti, Cintia S. de Paiva
The Ocular Surface.2021; 20: 139. CrossRef
Safety and Tolerability of an Eye Drop Based on 0.6% Povidone–Iodine Nanoemulsion in Dry Eye Patients
Giovanni William Oliverio, Rosaria Spinella, Elisa Imelde Postorino, Leandro Inferrera, Emanuela Aragona, Pasquale Aragona
Journal of Ocular Pharmacology and Therapeutics.2021; 37(2): 90. CrossRef
The ocular microbiome and microbiota and their effects on ocular surface pathophysiology and disorders
Pasquale Aragona, Christophe Baudouin, Jose M. Benitez del Castillo, Elisabeth Messmer, Stefano Barabino, Jesus Merayo-Lloves, Francoise Brignole-Baudouin, Leandro Inferrera, Maurizio Rolando, Rita Mencucci, Maria Rescigno, Stefano Bonini, Marc Labetoulle
Survey of Ophthalmology.2021; 66(6): 907. CrossRef
Differences in the eyelid and buccal microbiome of glaucoma patients receiving long-term administration of prostaglandin analog drops
Su-Ho Lim, Jong Hoon Shin, Ji-Woong Lee, Young Lee, Je Hyun Seo
Graefe's Archive for Clinical and Experimental Ophthalmology.2021; 259(10): 3055. CrossRef
Ocular Microbiota and Intraocular Inflammation
Jing Jing Li, Sanjun Yi, Lai Wei
Frontiers in Immunology.2020;[Epub] CrossRef

Mesorhizobium denitrificans sp. nov., a novel denitrifying bacterium isolated from sludge: Muhammad Zubair Siddiqi , Ngo Thi Phuong Thao , Gyumin Choi , Dae-Cheol Kim , Young-Woo Lee , Sang Young Kim , Ji-Hyang Wee , Wan-Taek Im; J. Microbiol. 2019;57(4):238-242. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8590-0

359 View
0 Download
14 Web of Science
14 Crossref

Abstract PDF

A Gram-stain-negative, non-spore-forming, facultative, rodshaped bacterium (designated LA-28T) was isolated from a sludge sample from a wastewater treatment plant in Hanam city, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-28T clustered with species of the genus Mesorhizobium and appeared closely related to M. jarvisii LMG 28313T (96.8%), M. waimense ICMP 19557T (96.7%), and M. huakuii LMG 14107T (96.7%). Growth occurs at 18– 40°C on R2A medium in the presence of 1–4% NaCl (w/v) and at pH 6–8. The DNA G+C content was 61.2 mol%, and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (> 5%) were C16:0, C19:0 ω8c cyclo, C18:1 ω7c 11-methyl, and C18:1 ω7c and/or C18:1 ω6c (summed feature 8). Major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidyl-N-methylethanolamine (PME), and phosphatidylcholine (PC). Physiological and biochemical characteristics indicated that strain LA-28T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium denitrificans sp. nov. is proposed. The type strain is LA-28T (= KACC 19675T = LMG 30806T).

Citations

Citations to this article as recorded by

Bioaugmented biological contact oxidation reactor for treating simulated textile dyeing wastewater
Hongyu Dong, Yonglan Tian, Jianjiang Lu, Jie Zhao, Yanbin Tong, Junfeng Niu
Bioresource Technology.2024; 404: 130916. CrossRef
Manganese reductive dissolution coupled to Sb mobilization in contaminated shooting range soil
Lara Costa, Mathieu Martinez, Marcel Suleiman, Rolf Keiser, Moritz Lehmann, Markus Lenz
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef
Evaluation of the performance of new plastic packing materials from plastic waste in biotrickling filters for odour removal
S. Sáez-Orviz, R. Lebrero, L. Terrén, S. Doñate, M.D. Esclapez, L. Saúco, R. Muñoz
Process Safety and Environmental Protection.2024; 191: 2361. CrossRef
Mesorhizobium koreense sp. nov., Isolated from Soil
Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
Journal of Microbiology and Biotechnology.2024; 34(9): 1819. CrossRef
Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer
Elena Colombi, Yvette Hill, Rose Lines, John T. Sullivan, MacLean G. Kohlmeier, Claus T. Christophersen, Clive W. Ronson, Jason J. Terpolilli, Joshua P. Ramsay
Microbial Genomics .2023;[Epub] CrossRef
Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov
Minkyung Kim, Wonjae Kim, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
The structure and assembly of rhizobacterial communities are influenced by poplar genotype
Qi Liang Zhu, Kun Yan, Nian Zhao Wang, Shu Qi Ma, De Shan Lu, Xiao Hua Su, Zheng Sai Yuan, Yu Feng Dong, Yan Ping Wang, Chang Jun Ding
Frontiers in Microbiology.2022;[Epub] CrossRef
Shifts of microbial community structure along substrate concentration gradients in immobilized biomass for nitrogen removal
Shao-Wei Tsai, Larissa Schwinghammer, Chien-Hsien Lee, Cheng-Fang Lin, Chia-Hung Hou
npj Clean Water.2022;[Epub] CrossRef
Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil
Ji-Yoon Kim, Kyung-Suk Cho
Scientific Reports.2022;[Epub] CrossRef
Aerobic granulation of nitrifying activated sludge enhanced removal of 17α-ethinylestradiol
Lili Wang, Zhifang Liu, Xiaoman Jiang, Anjie Li
Science of The Total Environment.2021; 801: 149546. CrossRef
Combined impacts of diclofenac and divalent copper on the nitrogen removal, bacterial activity and community from a sequencing batch reactor
Huan Yang, Zichao Wang, Shengyu Yuan, Yueyue Wang, Youtao Song, Naishun Bu, Lin Wang, Lu Zhang
Journal of Water Process Engineering.2021; 43: 102212. CrossRef
Nitrogen removal bacterial strains, MSNA-1 and MSD4, with wide ranges of salinity and pH resistances
Xiaoying Zeng, Jinhui Jeanne Huang, Binbin Hua, Pascale Champagne
Bioresource Technology.2020; 310: 123309. CrossRef
Metabolomics and metagenomics characteristic of historic beeswax seals
Justyna Szulc, Ivona Jablonskaja, Elżbieta Jabłońska, Tomasz Ruman, Joanna Karbowska-Berent, Beata Gutarowska
International Biodeterioration & Biodegradation.2020; 152: 105012. CrossRef
International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019
Philippe de Lajudie, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3563. CrossRef

Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean: Jaeho Song , Ilnam Kang , Yochan Joung , Susumu Yoshizawa , Ryo Kaneko , Kenshiro Oshima , Masahira Hattori , Koji Hamasaki , Soochan Kim , Kangseok Lee , Jang-Cheon Cho; J. Microbiol. 2019;57(5):413-422. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8712-8

328 View
0 Download
2 Web of Science
2 Crossref

Abstract PDF

Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC- 165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/ coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

Citations

Citations to this article as recorded by

Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef
Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents
Joel Slinger, James W. Wynne, Mark B. Adams
Frontiers in Animal Science.2021;[Epub] CrossRef

Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil: Yue Huo , Jong-Pyo Kang , Joon Hurh , Yaxi Han , Jong-Chan Ahn , Ramya Mathiyalagan , Chunhong Piao , Deok-Chun Yang; J. Microbiol. 2018;56(10):748-752. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8202-4

339 View
0 Download
3 Crossref

Abstract PDF

A Gram-negative, non-motile, aerobic, catalase-, and oxidasepositive bacterial strain, designated DCY117T, was isolated from ginseng cultivated soil in Gochang-gun, Republic of Korea, and was characterized taxonomically using a multifaceted approach. 16S rRNA gene sequence analysis revealed that strain DCY117T showed highest similarity to Lysobacter ruishenii CTN-1T (95.3%). Phylogenetic analysis revealed that closely related relatives of strain DCY117T were L. aestuarii S2-CT (95.1%), L. daejeonensis GH1-9T (95.0%), and L. caeni BUT-8T (94.9%). Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) were the major polar lipids of strain DCY117T. The major isoprenoid quinone was Q-8. The major cellular fatty acids of strain DCY117T were iso-C15:0, iso-C16:0, and summed feature 9 (comprising iso-C17:1 ω9c and/or 10-methyl-C16:0). Genomic DNA G + C content was 61.8 mol%. On the basis of our findings, strain DCY117T is a novel species in the genus Lysobacter. We propose the name Lysobacter panacihumi sp. nov., and the type strain is DCY117T (= KCTC 62019T = JCM 32168T).

Citations

Citations to this article as recorded by

Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
Journal of Microbiology.2021; 59(8): 709. CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease: Thi Thuy Tien Nguyen , Yuta Fujimura , Iyo Mimura , Yusuke Fujii , Ngoc Luong Nguyen , Kensuke Arakawa , Hidetoshi Morita; J. Microbiol. 2018;56(10):760-771. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8297-7

364 View
0 Download
21 Crossref

Abstract PDF

The group of butyrate-producing bacteria within the human gut microbiome may be associated with positive effects on memory improvement, according to previous studies on dementia- associated diseases. Here, fecal samples of four elderly Japanese diagnosed with Alzheimer’s disease (AD) were used to isolate butyrate-producing bacteria. 226 isolates were randomly picked, their 16S rRNA genes were sequenced, and assigned into sixty OTUs (operational taxonomic units) based on BLASTn results. Four isolates with less than 97% homology to known sequences were considered as unique OTUs of potentially butyrate-producing bacteria. In addition, 12 potential butyrate-producing isolates were selected from the remaining 56 OTUs based on scan-searching against the PubMed and the ScienceDirect databases. Those belonged to the phylum Bacteroidetes and to the clostridial clusters I, IV, XI, XV, XIVa within the phylum Firmicutes. 15 out of the 16 isolates were indeed able to produce butyrate in culture as determined by high-performance liquid chromatography with UV detection. Furthermore, encoding genes for butyrate formation in these bacteria were identified by sequencing of degenerately primed PCR products and included the genes for butyrate kinase (buk), butyryl-CoA: acetate CoAtransferase (but), CoA-transferase-related, and propionate CoA-transferase. The results showed that eight isolates possessed buk, while five isolates possessed but. The CoA-transfer- related gene was identified as butyryl-CoA:4-hydroxybutyrate CoA transferase (4-hbt) in four strains. No strains contained the propionate CoA-transferase gene. The biochemical and butyrate-producing pathways analyses of butyrate producers presented in this study may help to characterize the butyrate-producing bacterial community in the gut of AD patients.

Citations

Citations to this article as recorded by

Gut Microbiota and Alzheimer Disease
Lester Raymundo Dominguez Huarcaya
Acta Neurologica Taiwanica.2025; 34(1): 1. CrossRef
Polysaccharides from Trametes versicolor as a Potential Prebiotic to Improve the Gut Microbiota in High-Fat Diet Mice
Ming Bai, Zhenfeng Huang, Xiaoya Zheng, Mingyong Hou, Song Zhang
Microorganisms.2024; 12(8): 1654. CrossRef
Novel primers to identify a wider diversity of butyrate-producing bacteria
Xianbin Meng, Qinglong Shu
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Influence of gut microbiota on the development of most prevalent neurodegenerative dementias and the potential effect of probiotics in elderly: A scoping review
David Mateo, Montse Marquès, José L. Domingo, Margarita Torrente
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics.2024;[Epub] CrossRef
The Pathogenicity of Fusobacterium nucleatum Modulated by Dietary Fibers—A Possible Missing Link between the Dietary Composition and the Risk of Colorectal Cancer
Sadia Nawab, Qelger Bao, Lin-Hua Ji, Qian Luo, Xiang Fu, Shuxuan Fan, Zixin Deng, Wei Ma
Microorganisms.2023; 11(8): 2004. CrossRef
The Role of the Gut Microbiota and Microbial Metabolites in the Pathogenesis of Alzheimer’s Disease
Yi Wang
CNS & Neurological Disorders - Drug Targets.2023; 22(4): 577. CrossRef
Microbial-derived metabolites as a risk factor of age-related cognitive decline and dementia
Emily Connell, Gwenaelle Le Gall, Matthew G. Pontifex, Saber Sami, John F. Cryan, Gerard Clarke, Michael Müller, David Vauzour
Molecular Neurodegeneration.2022;[Epub] CrossRef
Research trend of microbiota-gut-brain axis in Alzheimer’s disease based on CiteSpace (2012–2021): A bibliometrics analysis of 608 articles
Zi-Long Li, Hao-Tian Ma, Meng Wang, Yi-Hua Qian
Frontiers in Aging Neuroscience.2022;[Epub] CrossRef
Marine Natural Products from the Russian Pacific as Sources of Drugs for Neurodegenerative Diseases
Yuri S. Khotimchenko, Denis N. Silachev, Vladimir L. Katanaev
Marine Drugs.2022; 20(11): 708. CrossRef
Therapeutic potential of short-chain fatty acid production by gut microbiota in neurodegenerative disorders
Sarika Yadav, Ashish Dwivedi, Anurag Tripathi, Amit Kumar Tripathi
Nutrition Research.2022; 106: 72. CrossRef
Interaction Between Diet and Microbiota in the Pathophysiology of Alzheimer’s Disease: Focus on Polyphenols and Dietary Fibers
Andrea Ticinesi, Leonardo Mancabelli, Luca Carnevali, Antonio Nouvenne, Tiziana Meschi, Daniele Del Rio, Marco Ventura, Andrea Sgoifo, Donato Angelino
Journal of Alzheimer's Disease.2022; 86(3): 961. CrossRef
Study on the Mechanism of Intestinal Microbiota in Alzheimer’s Disease
土玲车
Advances in Microbiology.2022; 11(04): 182. CrossRef
Diet-Microbiota-Brain Axis in Alzheimer’s Disease
Halle J. Kincaid, Ravinder Nagpal, Hariom Yadav
Annals of Nutrition and Metabolism.2021; 77(Suppl. 2): 21. CrossRef
Some Candidate Drugs for Pharmacotherapy of Alzheimer’s Disease
Barbara Miziak, Barbara Błaszczyk, Stanisław J. Czuczwar
Pharmaceuticals.2021; 14(5): 458. CrossRef
The impact of the microbiota-gut-brain axis on Alzheimer’s disease pathophysiology
Tejaswini Doifode, Vijayasree V. Giridharan, Jaqueline S. Generoso, Gursimrat Bhatti, Allan Collodel, Paul E. Schulz, Orestes V. Forlenza, Tatiana Barichello
Pharmacological Research.2021; 164: 105314. CrossRef
Alzheimer’s disease: The derailed repair hypothesis
Annette Offringa-Hup
Medical Hypotheses.2020; 136: 109516. CrossRef
Functional Foods: An Approach to Modulate Molecular Mechanisms of Alzheimer’s Disease
Anna Atlante, Giuseppina Amadoro, Antonella Bobba, Valentina Latina
Cells.2020; 9(11): 2347. CrossRef
Gut microbiota and pro/prebiotics in Alzheimer’s disease
Ryszard Pluta, Marzena Ułamek-Kozioł, Sławomir Januszewski, Stanisław J. Czuczwar
Aging.2020; 12(6): 5539. CrossRef
Draft Genome Sequence of Butyricimonas faecihominis 30A1, Isolated from Feces of a Japanese Alzheimer’s Disease Patient
Tien Thi Thuy Nguyen, Kenshiro Oshima, Hidehiro Toh, Anushka Khasnobish, Yusuke Fujii, Kensuke Arakawa, Hidetoshi Morita, Steven R. Gill
Microbiology Resource Announcements.2019;[Epub] CrossRef
Fecal metabolite of a gnotobiotic mouse transplanted with gut microbiota from a patient with Alzheimer’s disease
Yusuke Fujii, Thuy Tien Thi Nguyen, Yuta Fujimura, Naotaka Kameya, Shoji Nakamura, Kensuke Arakawa, Hidetoshi Morita
Bioscience, Biotechnology, and Biochemistry.2019; 83(11): 2144. CrossRef
Gut microbiota in common elderly diseases affecting activities of daily living
Yukihiro Shimizu
World Journal of Gastroenterology.2018; 24(42): 4750. CrossRef

Brevibacterium anseongense sp. nov., isolated from soil of ginseng field: Mi-Seon Jung , Xiao-Tian Quan , Muhammad Zubair Siddiqi , Qingzhen Liu , Sang Yong Kim , Ji-Hyang Wee , Wan Taek Im; J. Microbiol. 2018;56(10):706-712. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8181-5

331 View
1 Download
7 Crossref

Abstract PDF

A Gram-positive, aerobic, non-motile, pale-yellow, and rodshaped bacterium, designated as Gsoil 188T, was isolated from the soil of a ginseng field in Pocheon, South Korea. A phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to B. epidermidis NBRC 14811T (98.4%), B. sediminis FXJ8.269T (98.2%), B. avium NCFB 3055T (98.1%), and B. oceani BBH7T (98.1%), while it shared less than 98.1% identity with the other species of this genus. The DNA G + C content was 68.1 mol%. The predominant quinone was MK-8(H2). The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The cell wall peptidoglycan of strain Gsoil 188T contained meso-diaminopimelic acid. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminolipid. The physiological and biochemical characteristics, low DNA-DNA relatedness values, and taxonomic analysis allowed the differentiation of strain Gsoil 188T from the other recognized species of the genus Brevibacterium. Therefore, strain Gsoil 188T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium anseongense sp. nov. is proposed, with the type strain Gsoil 188T (= KACC 19439T = LMG 30331T).

Citations

Citations to this article as recorded by

Brevibacterium litoralis sp. nov., a cellulose-degrading strain isolated from marine surface sediment
Quan Yang, Aolin Zhao, Haifei Liu, Jiawei Li, Shujing Wu, Ying Huang, Jie Weng, Mingguo Jiang, Yi Jiang
Antonie van Leeuwenhoek.2025;[Epub] CrossRef
Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest
Mao Tian, Shiyu Wu, Wei Zhang, Gaosen Zhang, Xue Yu, Yujie Wu, Puchao Jia, Binglin Zhang, Tuo Chen, Guangxiu Liu
Journal of Microbiology.2024; 62(4): 277. CrossRef
Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces
Yuyuan Huang, Lingzhi Dong, Jian Gong, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Qianni Huang, Ji Pu, Liyun Liu, Jianguo Xu
Journal of Microbiology.2022; 60(10): 977. CrossRef
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Characterization of plant growth promoting activities of indigenous bacteria of phosphate mine wastes, a first step toward revegetation
Najoua Mghazli, Odile Bruneel, Rahma Zouagui, Rachid Hakkou, Laila Sbabou
Frontiers in Microbiology.2022;[Epub] CrossRef
Brevibacterium renqingii sp. nov., isolated from the Daqu of Baijiu
Yi Yan, Xuan Xing, Zhanbin Sun, Jia Li, Shuyue Hao, Jialiang Xu
Archives of Microbiology.2021; 203(5): 2291. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

Pedobacter aquicola sp. nov., isolated from freshwater: Yochan Joung , Hye-jin Jang , Miri Park , Jaeho Song , Jang-Cheon Cho; J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7499-3

353 View
0 Download
11 Crossref

Abstract PDF

A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).

Citations

Citations to this article as recorded by

Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
Nhan Le Thi Tuyet, Jaisoo Kim
Diversity.2024; 16(5): 292. CrossRef
Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil
Haejin Woo, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Yonghee Jung, Taegun Seo
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Screening of potential microbial markers for lung cancer using metagenomic sequencing
Qiang Chen, Kai Hou, Mingze Tang, Shuo Ying, Xiaoyun Zhao, Guanhua Li, Jianhui Pan, Xiaomin He, Han Xia, Yuechuan Li, Zheng Lou, Li Zhang
Cancer Medicine.2023; 12(6): 7127. CrossRef
Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2022; 115(3): 445. CrossRef
Pedobacter riviphilus sp. nov., isolated from stream sediment
Hong Sik Im, Yochan Joung, Sang-Seob Lee
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation
Cya-Yong Cho, So-Ra Han, Tae-Jin Oh
Current Microbiology.2021; 78(3): 944. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef
Pedobacter indicus sp. nov., isolated from deep-sea sediment
Xiao-yan He, Na Li, Xiu-lan Chen, Yu-zhong Zhang, Xi-ying Zhang, Xiao-yan Song
Antonie van Leeuwenhoek.2020; 113(3): 357. CrossRef
Leeia aquatica sp. nov., isolated from freshwater
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2020; 70(11): 5848. CrossRef
Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2020; 70(12): 6126. CrossRef
Rhodoferax lacus sp. nov., isolated from a large freshwater lake
Miri Park, Jaeho Song, Gi Gyun Nam, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2019; 69(10): 3135. CrossRef

Terrabacter ginsengisoli sp. nov., isolated from ginseng cultivating soil: Mei-Fang Jin , Xiao-Tian Quan , Muhammad Zubair Siddiqi , Qing-Zhen Liu , Hong-Shan Yu , Wan-Taek Im; J. Microbiol. 2018;56(5):331-336. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-8098-z

315 View
0 Download
3 Crossref

Abstract PDF

A Gram-positive, strictly aerobic, nonmotile, yellowish, coccus- rod-shaped bacterium (designated Gsoil 653T) isolated from ginseng cultivating soil was characterized using a polyphasic approach to clarify its taxonomic position. The strain Gsoil 653T exhibited optimal growth at pH 7.0 on R2A agar medium at 30°C. Phylogenetic analysis based on 16S rRNA gene sequence similarities, indicated that Gsoil 653T belongs to the genus Terrabacter of the family Humibacillus, and was closely related to Terrabacter tumescens DSM 20308T (98.9%), Terrabacter carboxydivorans PY2T (98.9%), Terrabacter terrigena ON10T (98.8%), Terrabacter terrae PPLBT (98.6%), and Terrabacter lapilli LR-26T (98.6%). The DNA G + C content was 70.5 mol%. The major quinone was MK-8(H4). The primary polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidyl-ethanolamine. The predominant fatty acids were iso-C15:0, iso-C16:0, iso-C14:0, and anteiso-C15:0, as in the case of genus Terrabacter, thereby supporting the categorization of strain Gsoil 653T. However, the DNA-DNA relatedness between Gsoil 653T and closely related strains of Terrabacter species was low at less than 31%. Moreover, strain Gsoil 653T could be both genotypically and phenotypically distinguished from the recognized species of the genus Terrabacter. This isolate, therefore, represents a novel species, for which the name Terrabacter ginsengisoli sp. nov. is proposed with the type strain Gsoil 653T (= KACC 19444T = LMG 30325T).

Citations

Citations to this article as recorded by

Phosphorus fertilizer application and tillage practices influence bacterial community composition: implication for soil health
R.A. Adeleke, C. C. Obieze, C. Mukoro, C. B. Chikere, S. Tsipinana, A. Nciizah
Archives of Agronomy and Soil Science.2023; 69(5): 803. CrossRef
Ecofriendly Synthesis of Silver Nanoparticles by Terrabacter humi sp. nov. and Their Antibacterial Application against Antibiotic-Resistant Pathogens
Shahina Akter, Sun-Young Lee, Muhammad Zubair Siddiqi, Sri Renukadevi Balusamy, Md. Ashrafudoulla, Esrat Jahan Rupa, Md. Amdadul Huq
International Journal of Molecular Sciences.2020; 21(24): 9746. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

Bacillus spongiae sp. nov., isolated from sponge of Jeju Island: Ga-Eun Lee , Wan-Taek Im , Jin-Sook Park; J. Microbiol. 2018;56(4):217-222. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7511-y

395 View
0 Download
2 Crossref

Abstract PDF

A Gram-reaction-positive, strictly aerobic, motile, endospore- forming, and rod-shaped bacterial strain designated 135PIL107-10T was isolated from a sponge on Jeju Island, and its taxonomic position was investigated using a polyphasic approach. Strain 135PIL107-10T grew at 20–37°C (optimum temperature, 25°C) and pH 6.0–10.0 (optimum pH, 6.0) on marine and R2A agars. Based on 16S rRNA gene phylogeny analysis, the novel strain formed a new branch within the genus Bacillus of the family Bacillaceae, and formed clusters with Bacillus thaohiensis NHI-38T (96.8%), Bacillus fengqiuensis NPK15T (96.7%), and Bacillus songklensis CAU 1033T (96.7%). Lower sequence similarities (97.0%) were found with the type strains of all other recognized members of the genus Bacillus (95.6–96.8% similarity). The G + C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was menaquinone-7 and the major fatty acids were iso-C15:0 and iso-C17:1ω10c. The overall polar lipid patterns were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The isolate therefore represents a novel species, for which the name Bacillus spongiae sp. nov. is proposed, with the type strain 135PIL107-10T (= KACC 19275T = LMG 30080T).

Citations

Citations to this article as recorded by

Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China
Lei Chen, Xue-Ning Wang, Hong-Yu Bi, Guang-Yu Wang
Marine Drugs.2022; 20(10): 588. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

Lysobacter spongiae sp. nov., isolated from spongin: Heejae Choi , Wan-Taek Im , Jin-Sook Park; J. Microbiol. 2018;56(2):97-103. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7462-3

343 View
0 Download
10 Crossref

Abstract PDF

A Gram-negative, motile, aerobic and rod-shaped bacterial strain designated 119BY6-57T was isolated from spongin. The taxonomic position of the novel isolate was confirmed using the polyphasic approach. Strain 119BY6-57T grew well at 25– 30°C on marine agar. On the basis of 16S rRNA gene sequence similarity, strain 119BY6-57T belongs to the family Xanthomonadaceae and is related to Lysobacter aestuarii S2-CT (99.8% sequence similarity), L. maris KMU-14T (97.5%), and L. daejeonensis GH1-9T (97.3%). Lower sequence similarities (97.0%) were found with all of the other recognized members of the genus Lysobacter. The G + C content of the genomic DNA was 69.9 mol%. The major respiratory quinone was Q-8 and the major fatty acids were C16:0 iso, C15:0 iso, summed feature 9 (comprising C17􍾙:1 iso ω9c and/or C16:0 10-methyl), summed feature 3 (comprising C16􍾙:1 ω7c and/or C16:1 ω6c), and C11:0 iso 3-OH. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, and an unidentified polar lipid. DNADNA relatedness values between strain 119BY6-57T and its closest phylogenetically neighbors were below 48.0 ± 2.1%. Based on genotypic and phenotypic characteristics, it is concluded that strain 119BY6-57T is a new member within the genus Lysobacter, for which the name Lysobacter spongiae sp. nov. is proposed. The type strain is 119BY6-57T (= KACC 19276T = LMG 30077T).

Citations

Citations to this article as recorded by

Extended-Spectrum Beta-Lactamase Producing Escherichia coli in Raw Cow Milk At Selling Points and Determinants of Contamination in and Around Chencha, Southern Ethiopia
Tomas Torka
Veterinary Medicine: Research and Reports.2024; Volume 15: 159. CrossRef
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China
Bang-Yan Niu, Dong-Jun Ren, Fang-Bo Zhang, Hong-Tu Zhu, Hai-Lei Wei, Ming-Chao Ma, Miao Gao
Folia Microbiologica.2023; 68(6): 991. CrossRef
An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota ) Isolated from Aquatic Host Species Described in 2018 to 2021
Claire R. Burbick, Erik Munson, Sara D. Lawhon, Amanda Zapp, Maia Villaflor, Elizabeth Thelen, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Parvicella tangerina gen. nov., sp. nov. (Parvicellaceae fam. nov., Flavobacteriales), first cultured representative of the marine clade UBA10066, and Lysobacter luteus sp. nov., from activated sludge of a seawater-processing wastewater treat
Teresa Lucena, Olga Sánchez, Isabel Sanz-Saez, Silvia G. Acinas, Laura Garrido, Jordi Mas, M. Carmen Macián, María A. Ruvira, David R. Arahal, María J. Pujalte
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
Journal of Microbiology.2021; 59(8): 709. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef
Lysobacter penaei sp. nov., isolated from intestinal content of a Pacific white shrimp (Penaeus vannamei)
Shuaishuai Xu, Anzhang Li, Ming-Xia Zhang, Qing Yao, Honghui Zhu
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil
Yue Huo, Jong-Pyo Kang, Joon Hurh, Yaxi Han, Jong-Chan Ahn, Ramya Mathiyalagan, Chunhong Piao, Deok-Chun Yang
Journal of Microbiology.2018; 56(10): 748. CrossRef

Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.: Dong-Shan An , Muhammad Zubair Siddiqi , Kyoung-Ho Kim , Hong-Shan Yu , Wan-Taek Im; J. Microbiol. 2018;56(1):24-29. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7107-6

362 View
0 Download
7 Crossref

Abstract PDF

A taxonomic study was conducted on BR7-21T, a bacterial strain isolated from the soil of a ginseng field in Baekdu Mountain. Comparative studies of the 16S rRNA gene sequence showed that the isolate was most closely related to Conexibacter woesei DSM 14684T, Solirubrobacter pauli ATCC BAA-492T, Patulibacter minatonensis JCM 12834T, with 93.8%, 92.4%, and 91.5% sequence similarity, respectively; each genus represented a family in the order Solirubrobacterales. Strain BR7-21T was Gram-reaction positive, non-spore forming, aerobic, non-motile, and short rod-shaped. It grew well on half-strength R2A medium. The G + C content of the genomic DNA was 73.9%. It contained meso-diaminopimelic acid in the cell wall and the major menaquinones were MK-7(H4) and MK-8(H4). The major fatty acids were summarized as (C16:1 ω7c/iso-C15:0 2-OH), iso-C16:0, and C17:0 cyclo. On the basis of polyphasic evidence, it was proposed that strain BR7- 21T should be placed in a new genus and species, for which the name Baekduia soli gen. nov., sp. nov. was proposed with the type strain BR7-21T (= KCTC 22257T = LMG 24797T). The family Baekduiaceae fam. nov. is proposed to encompass the genus Baekduia gen. nov.

Citations

Citations to this article as recorded by

Actinomycetota bioprospecting from ore-forming environments
César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy Parkinson
Microbial Genomics .2024;[Epub] CrossRef
Svornostia abyssi gen. nov., sp. nov. isolated from the world’s deepest silver–uranium mine currently devoted to the extraction of radon-saturated water
Gabriela Kapinusova, Jachym Suman, Michal Strejcek, Petr Pajer, Tomas Cajthaml, Pavel Ulbrich, Meina Neumann-Schaal, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Baekduia alba sp. nov., a novel representative of the order Solirubrobacterales isolated from temperate grassland soil
Selma Vieira, Katharina J. Huber, Alicia Geppert, Jacqueline Wolf, Meina Neumann-Schaal, Mathias Müsken, Jörg Overmann
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil
Chol Song Kim, Zhenyu Liu, Xiaoya Peng, Kun Qin, Jun Huang, Jingjing Niu, Yixuan Liu, Jia Liu, Mingjing Sun, Fang Peng
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
High-Resolution Indicators of Soil Microbial Responses to N Fertilization and Cover Cropping in Corn Monocultures
Nakian Kim, Chance W. Riggins, María C. Zabaloy, Marco Allegrini, Sandra L. Rodriguez-Zas, María B. Villamil
Agronomy.2022; 12(4): 954. CrossRef
Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil
Selma Vieira, Katharina J. Huber, Alicia Geppert, Jacqueline Wolf, Meina Neumann-Schaal, Manja Luckner, Gerhard Wanner, Mathias Müsken, Jörg Overmann
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

Cecal microbiome divergence of broiler chickens by sex and body weight: Kyu-Chan Lee , Dong Yong Kil , Woo Jun Sul; J. Microbiol. 2017;55(12):939-945. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7202-0

393 View
0 Download
83 Crossref

Abstract PDF

The divergence of gut bacterial community on broiler chickens has been reported as potentially possible keys to enhancing nutrient absorption, immune systems, and increasing poultry health and performance. Thus, we compared cecal bacterial communities and functional predictions by sex and body weight regarding the association between cecal microbiota and chicken growth performance. In this study, a total of 12 male and 12 female 1-day-old broiler chickens were raised for 35 days in 2 separate cages. Chickens were divided into 3 subgroups depending on body weight (low, medium, and high) by each sex. We compared chicken cecal microbiota compositions and its predictive functions by sex and body weight difference. We found that bacterial 16S rRNA genes were classified as 3 major phyla (Bacteroidetes, Firmicutes, and Proteobacteria), accounting for > 98% of the total bacterial community. The profiling of different bacterial taxa and predictive metagenome functions derived from 16S rRNA genes were performed over chicken sex and bodyweight. Male chickens were related to the enrichment of Bacteroides while female chickens were to the enrichment of Clostridium and Shigella. Male chickens with high body weight were associated with the enrichment of Faecalibacterium and Shuttleworthia. Carbohydrate and lipid metabolisms were suggested as candidate functions for weight gain in the males. This suggests that the variation of cecal bacterial communities and their functions by sex and body weight may be associated with the differences in the growth potentials of broiler chickens.

Citations

Citations to this article as recorded by

Anticoccidial activities of a multicomplex mineral-based diet in broilers infected with Eimeria acervulina
Binh T. Nguyen, Rochelle A. Flores, Paula Leona T. Cammayo-Fletcher, Suk Kim, Woo H. Kim, Wongi Min
Parasites, Hosts and Diseases.2025; 63(2): 135. CrossRef
Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights
Hongjiao Wang, Long Li, Jinhai Wu, Xuefeng Yuan, Liang Hong, Lei Pu, Shunyi Qin, Liuan Li, Hua Yang, Jianbin Zhang
Poultry Science.2025; 104(8): 105275. CrossRef
Impact of stocking densities on growth, organ index, serum biochemistry, gut morphology and microbiota of young ducks in a rice-duck-crayfish coculture system
Xiao Long He, Zhen Hua Liang, Ze Heng Huang, Lian Bing Qi, Yan Wu, Jia Liu, Tao Huang, Jing Bo Liu, Jin Song Pi, Hao Zhang
Animal Bioscience.2025; 38(5): 1067. CrossRef
Niacin mitigates heat stress-induced reduction in performance of Taihe black-boned silky fowl through modulation of gut microorganisms and short-chain fatty acids
Wenliang Mei, Chuanbin Chen, Xiaona Gao, Wenyan Zhang, Ziyu Hu, Mingren Qu, Gen Wan, Lanjiao Xu
Frontiers in Veterinary Science.2025;[Epub] CrossRef
Impact of attapulgite loaded with essential oil in diets on the growth performance and gut microbiota of broilers: a correlation analysis
Changqing He, Hanxiang Du, Lingyun He, Yi Liu, Jing Shan, Xiangyong Qu, Songchang Guo, Meichun Li, Jia Tang
Italian Journal of Animal Science.2025; 24(1): 1155. CrossRef
Effects of purple corn anthocyanin on slaughter performance, immune function, the caecal microbiota and the transcriptome in chickens
Xingzhou Tian, Chao Ban, Di Zhou, Hui Li, Jiaxuan Li, Xu Wang, Qi Lu
Poultry Science.2025; 104(6): 105104. CrossRef
Impact of Chlorella vulgaris and probiotic supplementation on performance, immunity and intestinal microbiota of broiler chickens
Verena Pereira Dinalli, Marcio Carvalho Costa, Emerson José Venâncio, João Antônio Barbosa Filho, José Antônio Bessegatto, Augusto Tasch Holkem, Amauri Alcindo Alfieri, Caio Abercio da Silva, Alexandre Oba, Arda Yildirim
PLOS ONE.2025; 20(1): e0313736. CrossRef
Gut response to the dietary supplementation with sodium butyrate in broiler chickens: morphology and microbiota composition and predictive functional groups
Giulia Zardinoni, Almudena Huerta, Marija Boskovic Cabrol, Angela Trocino, Elisa Fonsatti, Cristina Ballarin, Martina Bortoletti, Marco Birolo, Francesco Bordignon, Piergiorgio Stevanato, Daniel Julian, Gerolamo Xiccato
Italian Journal of Animal Science.2025; 24(1): 123. CrossRef
Red seaweed Chondracanthus chamissoi supplementation improved the growth performance of broiler chickens partially through effects on intestinal morphology and cecal microbiota
O.S. Olowe, T. Johnson, O. Adeola
Poultry Science.2025; 104(9): 105402. CrossRef
Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecal microbiome
Yong Yue, Bingnong Yao, Fuyou Liao, Zhiqiang He, Papungkorn Sangsawad, Shenglin Yang
Scientific Reports.2025;[Epub] CrossRef
Breast muscle myopathies: twists and turns in modern broilers
Elizabeth S. Greene, Sunoh Che, Francesca Soglia, Tomohito Iwasaki, Takafumi Watanabe, Takeshi Kawasaki, Leonardo Susta, Massimiliano Petracci, Colin Scanes, Sami Dridi
Avian Pathology.2025; 54(6): 669. CrossRef
Broiler chickens’ responses to a diet incorporating fermented or unfermented palm kernel cake on intestinal morphology, antioxidant indices, caecal microbiota composition, and liver metabolomic profiles
Sindaye Daniel, Shehata Zeid, Liao Jinghong, Suqin Hang
Italian Journal of Animal Science.2025; : 1. CrossRef
Dietary ethylenediamine dihydroiodide mitigated Escherichia coli O78-induced immune and intestinal damage of ducks via suppression of NF-κB signal
Yanru Liang, Yaqi Chang, Yueqin Xie, Qinteng Hou, Hua Zhao, Guangmang Liu, Xiaoling Chen, Gang Tian, Jingyi Cai, Gang Jia
Poultry Science.2024; 103(5): 103610. CrossRef
The effect of sex and dietary crude protein level on nutrient transporter gene expression and cecal microbiota populations in broiler chickens
Ashley D. England, Sara de las Heras-Saldana, Kosar Gharib-Naseri, Sarbast K. Kheravii, Shu-Biao Wu
Poultry Science.2024; 103(2): 103268. CrossRef
Morphological features of the feral pigeon’s (Columba livia f. urbana) digestive system
I. O. Кolomak
Journal for Veterinary Medicine, Biotechnology and Biosafety.2024; 10(1): 7. CrossRef
Microbial community profiling in intestinal tract of indigenous chickens from different villages
Mokoma Eunice Mootane, Thendo Mafuna, Tondani Madeleine Ramantswana, Dikeledi Petunia Malatji
Scientific Reports.2024;[Epub] CrossRef
The Effect of including a Mixed-Enzyme Product in Broiler Diets on Performance, Metabolizable Energy, Phosphorus and Calcium Retention
Harriet Walker, Suvi Vartiainen, Juha Apajalahti, Jules Taylor-Pickard, Ivana Nikodinoska, Colm A. Moran
Animals.2024; 14(2): 328. CrossRef
Integrating microbial 16S rRNA sequencing and non-targeted metabolomics to reveal sexual dimorphism of the chicken cecal microbiome and serum metabolome
Yongxian Yang, Fuping Zhang, Xuan Yu, Liqi Wang, Zhong Wang
Frontiers in Microbiology.2024;[Epub] CrossRef
Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens
Calvin Ho-Fung Lau, Sabrina Capitani, Yuan-Ching Tien, Lou Ann Verellen, Munene Kithama, Hellen Kang, Elijah G. Kiarie, Edward Topp, Moussa S. Diarra, Michael Fruci
Animal Microbiome.2024;[Epub] CrossRef
Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers
Muhammad Zeeshan Akram, Ester Arévalo Sureda, Luke Comer, Matthias Corion, Nadia Everaert
Animal Microbiome.2024;[Epub] CrossRef
Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?
Kateřina Marková, Jakub Kreisinger, Michal Vinkler
Poultry Science.2024; 103(6): 103752. CrossRef
Sex‐specific genetic parameter estimates of body weight in Mazandaran indigenous chickens
Mohammad Esmaeili, Mohsen Gholizadeh, Hasan Hafezian, Ayoub Farhadi
Journal of Animal Breeding and Genetics.2024; 141(4): 465. CrossRef
A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome
Xinwei Xiong, Yousheng Rao, Jinge Ma, Zhangfeng Wang, Qin He, Jishang Gong, Wentao Sheng, Jiguo Xu, Xuenong Zhu, Yuwen Tan, Yanbei Yang
Poultry Science.2023; 102(10): 102931. CrossRef
Plant essential oils improve growth performance by increasing antioxidative capacity, enhancing intestinal barrier function, and modulating gut microbiota in Muscovy ducks
Chaoyue Ge, Xinyu Luo, Lianchi Wu, Yujie Lv, Zhaoying Hu, Dongyou Yu, Bing Liu
Poultry Science.2023; 102(8): 102813. CrossRef
The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers
Walid Ghazi Al Hakeem, Keila Y. Acevedo Villanueva, Ramesh K. Selvaraj
Vaccines.2023; 11(3): 595. CrossRef
Growing Patterns of the Branca Chicken Breed—Concentrate vs. Maize-Based Diet
Laura Soares, Fernando Mata, Joaquim L. Cerqueira, José Araújo
Agriculture.2023; 13(12): 2282. CrossRef
Regulation of poultry lipid metabolism by dietary fibre: a review
Hua Zhou, Lei Yang, Tiande Zou, Qiufen Li, Mingren Qu, Jingming You, Guanhong Li
World's Poultry Science Journal.2023; 79(3): 485. CrossRef
Effect of water supplementation of Magic oil at different growing periods on growth performance, carcass traits, blood biochemistry, and ileal histomorphology of broiler chickens
Elsayed O.S. Hussein, Gamaleldin M. Suliman, Abdullah N. Al-Owaimer, Hani H. Al-Baadani, Maged A. Al-Garadi, Hani A. Ba-Awadh, Mohammed M. Qaid, Ayman A. Swelum
Poultry Science.2023; 102(8): 102775. CrossRef
Versatile, vigilance, and gut microbiome support the priority of high-ranking hens
Zhijiang Xie, Limin Xing, Mengqiao Zhao, Lei Zhao, Jinling Liu, Yushan Li, Jiankang Gan, Siyu Chen, Hua Li
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Anaerobutyricum and Subdoligranulum Are Differentially Enriched in Broilers with Disparate Weight Gains
Jing Liu, Kelsy Robinson, Wentao Lyu, Qing Yang, Jing Wang, Karen D. Christensen, Guolong Zhang
Animals.2023; 13(11): 1834. CrossRef
Inonotus obliquus polysaccharide are linear molecules that alter the abundance and composition of intestinal microbiota in Sprague Dawley rats
Songqing Liu, Wenjing Zhou, Xin Deng, Wei Jiang, Yanping Wang, Jiasui Zhan, Binhong Hu
Frontiers in Nutrition.2023;[Epub] CrossRef
Host genotype affects endotoxin release in excreta of broilers at slaughter age
F. Marcato, J. M. J. Rebel, S. K. Kar, I. M. Wouters, D. Schokker, A. Bossers, F. Harders, J. W. van Riel, M. Wolthuis-Fillerup, I. C. de Jong
Frontiers in Genetics.2023;[Epub] CrossRef
Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens
Michael H. Kogut, Mariano Enrique Fernandez Miyakawa
Animals.2023; 13(18): 2824. CrossRef
Long-Term Dietary Fish Meal Substitution with the Black Soldier Fly Larval Meal Modifies the Caecal Microbiota and Microbial Pathway in Laying Hens
Junliang Zhao, Takuma Ban, Hironori Miyawaki, Hirofumi Hirayasu, Akihisa Izumo, Shun-ichiro Iwase, Koji Kasai, Kiyonori Kawasaki
Animals.2023; 13(16): 2629. CrossRef
Sex-based responses of heat stress and subsequent recovery on the growth performance, metabolic changes, and redox status of broilers at market age
Ding Jinxue, Sun Shiang, Song Kai, Xiong Yongjie, He Shaojun
International Journal of Biometeorology.2023; 67(10): 1669. CrossRef
Dietary fiber modulates abdominal fat deposition associated with cecal microbiota and metabolites in yellow chickens
Xiaoyan Cui, Zhongyong Gou, Zongyong Jiang, Long Li, Xiajing Lin, Qiuli Fan, Yibing Wang, Shouqun Jiang
Poultry Science.2022; 101(4): 101721. CrossRef
Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens
Samson Oladokun, K. Fraser Clark, Deborah I. Adewole
Microorganisms.2022; 10(5): 861. CrossRef
Effect of stocking density on performance, meat quality and cecal bacterial communities of yellow feather broilers
Laidi Wang, Lingling Kong, Xiaodan Hu, Hao Bai, Zhixiu Wang, Yong Jiang, Yulin Bi, Guobin Chang, Guohong Chen
Animal Biotechnology.2022; 33(6): 1322. CrossRef
Potential Probiotics Role in Excluding Antibiotic Resistance
Irfan Ahmed, Zhengtian Li, Sharoon Shahzad, Saima Naveed, Ahmad Kamran Khan, Ayesha Ahmed, Zahid Kamran, Muhammad Yousaf, Shakeel Ahmad, Gulnaz Afzal, Hafiz Ishfaq Ahmad, Nasim Ahmad Yasin, Junjing Jia, Mubashir Hussain, Shahzad Munir, Ali Akbar
Journal of Food Quality.2022; 2022: 1. CrossRef
Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens
Monika Proszkowiec-Weglarz, Katarzyna B. Miska, Laura E. Ellestad, Lori L. Schreier, Stanislaw Kahl, Nadia Darwish, Philip Campos, Jonathan Shao
BMC Microbiology.2022;[Epub] CrossRef
Effect of Two Soybean Varieties Treated with Different Heat Intensities on Ileal and Caecal Microbiota in Broiler Chickens
Florian Hemetsberger, Benjamin Zwirzitz, Nadia Yacoubi, Wolfgang Kneifel, Karl Schedle, Konrad J. Domig
Animals.2022; 12(9): 1109. CrossRef
Comparison of organic acids supplementation on the growth performance, intestinal characteristics and morphology, and cecal microflora in broilers fed corn-soybean meal diet
Hao Yang Sun, Hong Bin Zhou, Yang Liu, Yue Wang, Cheng Zhao, Liang Mei Xu
Animal Bioscience.2022; 35(11): 1689. CrossRef
Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance
Yugal Raj Bindari, Priscilla F. Gerber
Poultry Science.2022; 101(1): 101612. CrossRef
A carvacrol-based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens
Marion Allaoua, Elsa Bonnafé, Pierre Etienne, Virginie Noirot, Jean-François Gabarrou, Adrien Castinel, Géraldine Pascal, Vincent Darbot, Michel Treilhou, Sylvie Combes
Journal of Applied Microbiology.2022; 132(6): 4501. CrossRef
The replacement of bacitracin methylene disalicylate with Bacillus subtilis PB6 in the diet of male Cherry Valley Ducks reduces the feed conversion ratio by improving intestinal health and modulating gut microbiota
Qianqian Zhang, Jian Li, Guixiang Wang, Lizhi Wang, Zhiming Zhang, Zhengfeng Fang, Yan Lin, Shengyu Xu, Bin Feng, Yong Zhuo, Lun Hua, Xuemei Jiang, Xilun Zhao, De Wu, Lianqiang Che
Poultry Science.2022; 101(11): 102155. CrossRef
Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics
Núria Tous, Sofia Marcos, Farshad Goodarzi Boroojeni, Ana Pérez de Rozas, Jürgen Zentek, Andone Estonba, Dorthe Sandvang, M. Thomas P. Gilbert, Enric Esteve-Garcia, Robert Finn, Antton Alberdi, Joan Tarradas
Frontiers in Physiology.2022;[Epub] CrossRef
Role of Physiology, Immunity, Microbiota, and Infectious Diseases in the Gut Health of Poultry
Samiru S. Wickramasuriya, Inkyung Park, Kyungwoo Lee, Youngsub Lee, Woo H. Kim, Hyoyoun Nam, Hyun S. Lillehoj
Vaccines.2022; 10(2): 172. CrossRef
The avian gut microbiota: Diversity, influencing factors, and future directions
Fengfei Sun, Junfeng Chen, Kai Liu, Meizhen Tang, Yuewei Yang
Frontiers in Microbiology.2022;[Epub] CrossRef
A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae
Johann Detilleux, Nassim Moula, Edwin Dawans, Bernard Taminiau, Georges Daube, Pascal Leroy
Biology.2022; 11(3): 357. CrossRef
Feed Safety and the Development of Poultry Intestinal Microbiota
Dragana Stanley, Yadav Sharma Bajagai
Animals.2022; 12(20): 2890. CrossRef
Factors Affecting Breast Myopathies in Broiler Chickens and Quality of Defective Meat: A Meta-Analysis
Francesco Bordignon, Gerolamo Xiccato, Marija Boskovic Cabrol, Marco Birolo, Angela Trocino
Frontiers in Physiology.2022;[Epub] CrossRef
Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens
Seyed Hossien Kairmi, Khaled Taha-Abdelaziz, Alexander Yitbarek, Mehdi Sargolzaei, Heidi Spahany, Jake Astill, Bahram Shojadoost, Mohammadali Alizadeh, Raveendra R. Kulkarni, John Parkinson, Shayan Sharif
Poultry Science.2022; 101(6): 101864. CrossRef
Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas
Priscila Fregulia, Mariana Magalhães Campos, Roberto Júnio Pedroso Dias, Junhong Liu, Wei Guo, Luiz Gustavo Ribeiro Pereira, Marco Antônio Machado, Daniele Ribeiro de Lima Reis Faza, Le Luo Guan, Phil C. Garnsworthy, André Luis Alves Neves
Frontiers in Microbiology.2022;[Epub] CrossRef
Effect of Salmonella Typhimurium Colonization on Microbiota Maturation and Blood Leukocyte Populations in Broiler Chickens
Kelsy Robinson, Anna L. F. V. Assumpcao, Komala Arsi, Gisela F. Erf, Annie Donoghue, Palmy R. R. Jesudhasan
Animals.2022; 12(20): 2867. CrossRef
Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal
Peter Kotsoana Montso, Caven Mguvane Mnisi, Ayansina Segun Ayangbenro
Frontiers in Microbiology.2022;[Epub] CrossRef
Microbiota populations and short-chain fatty acids production in cecum of immunosuppressed broilers consuming diets containing γ-irradiated Astragalus polysaccharides
Y.S. Liu, S. Li, X.F. Wang, T. Xing, J.L. Li, X.D. Zhu, L. Zhang, F. Gao
Poultry Science.2021; 100(1): 273. CrossRef
Effects of Clostridium butyricum, Sodium Butyrate, and Butyric Acid Glycerides on the Reproductive Performance, Egg Quality, Intestinal Health, and Offspring Performance of Yellow-Feathered Breeder Hens
Yibing Wang, Yang Wang, Xiajing Lin, Zhongyong Gou, Qiuli Fan, Shouqun Jiang
Frontiers in Microbiology.2021;[Epub] CrossRef
The link between broiler flock heterogeneity and cecal microbiome composition
Randi Lundberg, Christian Scharch, Dorthe Sandvang
Animal Microbiome.2021;[Epub] CrossRef
Changes in the ceca microbiota of broilers vaccinated for coccidiosis or supplemented with salinomycin
C. Orso, T.B. Stefanello, C.H. Franceschi, M.B. Mann, A.P.M. Varela, I.M.S. Castro, J. Frazzon, A.P.G. Frazzon, I. Andretta, A.M.L. Ribeiro
Poultry Science.2021; 100(4): 100969. CrossRef
Highly Fermentable Fiber Alters Fecal Microbiota and Mitigates Swine Dysentery Induced by Brachyspira hyodysenteriae
Emma T. Helm, Nicholas K. Gabler, Eric. R. Burrough
Animals.2021; 11(2): 396. CrossRef
Sex differences in growth performance are related to cecal microbiota in chicken
Lei Cui, Xiaolong Zhang, Ranran Cheng, Abdur Rahman Ansari, Abdelmotaleb A. Elokil, Yafang Hu, Yan Chen, Abdallah A. Nafady, Huazhen Liu
Microbial Pathogenesis.2021; 150: 104710. CrossRef
Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail
Jing-E Ma, Xin-Wei Xiong, Ji-Guo Xu, Ji-Shang Gong, Jin Li, Qiao Xu, Yuan-Fei Li, Yang-Bei Yang, Min Zhou, Xue-Nong Zhu, Yu-Wen Tan, Wen-Tao Sheng, Zhang-Feng Wang, Xu-Tang Tu, Cheng-Yao Zeng, Xi-Quan Zhang, You-Sheng Rao
Frontiers in Veterinary Science.2021;[Epub] CrossRef
The digestive and reproductive tract microbiotas and their association with body weight in laying hens
Yuan Su, Yile Ge, Zhongxian Xu, Dejing Zhang, Diyan Li
Poultry Science.2021; 100(11): 101422. CrossRef
Factors Influencing the Succession of the Fecal Microbiome in Broilers
Dirkjan Schokker, Britt de Klerk, Randy Borg, Alex Bossers, Johanna M.J. Rebel
Livestock Science.2021; 247: 104486. CrossRef
Effects of Xylanase in Corn- or Wheat-Based Diets on Cecal Microbiota of Broilers
Jian Wang, Heng Cao, Chengling Bao, Yajing Liu, Bing Dong, Chunlin Wang, Zhenda Shang, Yunhe Cao, Suozhu Liu
Frontiers in Microbiology.2021;[Epub] CrossRef
Effects of rearing system (floor vs. cage) and sex on performance, meat quality and enteric microorganism of yellow feather broilers
Lai-di WANG, Yang ZHANG, Ling-ling KONG, Zhi-xiu WANG, Hao BAI, Yong JIANG, Yu-lin BI, Guo-bin CHANG, Guo-hong CHEN
Journal of Integrative Agriculture.2021; 20(7): 1907. CrossRef
A reasonable correlation between cloacal and cecal microbiomes in broiler chickens
Nadia A. Andreani, Caroline J. Donaldson, Matthew Goddard
Poultry Science.2020; 99(11): 6062. CrossRef
Green Tea and Pomegranate Extract Administered During Critical Moments of the Production Cycle Improves Blood Antiradical Activity and Alters Cecal Microbial Ecology of Broiler Chickens
Vera Perricone, Marcello Comi, Carlotta Giromini, Raffaella Rebucci, Alessandro Agazzi, Giovanni Savoini, Valentino Bontempo
Animals.2020; 10(5): 785. CrossRef
Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics
Kara J. M. Taylor, John M. Ngunjiri, Michael C. Abundo, Hyesun Jang, Mohamed Elaish, Amir Ghorbani, Mahesh KC, Bonnie P. Weber, Timothy J. Johnson, Chang-Won Lee, Edward G. Dudley
Applied and Environmental Microbiology.2020;[Epub] CrossRef
Metagenomic analysis reveals linkages between cecal microbiota and feed efficiency in Xiayan chickens
Wenya Du, Jixian Deng, Zhuliang Yang, Linghu Zeng, Xiurong Yang
Poultry Science.2020; 99(12): 7066. CrossRef
Effects of Rearing Conditions and Sex on Cecal Microbiota in Ducks
Chunhong Zhu, Wenjuan Xu, Zhiyun Tao, Weitao Song, Hongxiang Liu, Shuangjie Zhang, Huifang Li
Frontiers in Microbiology.2020;[Epub] CrossRef
Effects of Eimeria maxima and Clostridium perfringens infections on cecal microbial composition and the possible correlation with body weight gain in broiler chickens
Mingmin Lu, Robert W. Li, Hongyan Zhao, Xianghe Yan, Hyun S. Lillehoj, Zhifeng Sun, SungTak Oh, Yueying Wang, Charles Li
Research in Veterinary Science.2020; 132: 142. CrossRef
Family matters: skin microbiome reflects the social group and spatial proximity in wild zebra finches
Kathrin Engel, Helga Pankoke, Sebastian Jünemann, Hanja B. Brandl, Jan Sauer, Simon C. Griffith, Jörn Kalinowski, Barbara A. Caspers
BMC Ecology.2020;[Epub] CrossRef
Dissection of the cecal microbial community in chickens after Eimeria tenella infection
Hong-Liang Chen, Xin-Yu Zhao, Guang-Xun Zhao, Hai-Bin Huang, Hao-Rui Li, Chun-Wei Shi, Wen-Tao Yang, Yan-Long Jiang, Jian-Zhong Wang, Li-Ping Ye, Quan Zhao, Chun-Feng Wang, Gui-Lian Yang
Parasites & Vectors.2020;[Epub] CrossRef
Dietary supplementation with fermented defatted “alperujo” induces modifications of the intestinal mucosa and cecal microbiota of broiler chickens
Agustín Rebollada-Merino, María Ugarte-Ruiz, Marta Hernández, Pedro Miguela-Villoldo, David Abad, Pedro Cuesta-Álvaro, David Rodríguez-Lázaro, Lucía de Juan, Lucas Domínguez, Antonio Rodríguez-Bertos
Poultry Science.2020; 99(11): 5308. CrossRef
Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers
Shengru Wu, Xiaodong Chen, Taohuan Li, Hao Ren, Lixin Zheng, Xiaojun Yang
Journal of Animal Science and Biotechnology.2020;[Epub] CrossRef
Sanguinarine modulate gut microbiome and intestinal morphology to enhance growth performance in broilers
Zhu-Ying Liu, Xiao-Long Wang, Shu-Qi Ou, De-Xing Hou, Jian-Hua He, Michael H. Kogut
PLOS ONE.2020; 15(6): e0234920. CrossRef
Characterization of heat stress affecting the growth performance, blood biochemical profile, and redox status in male and female broilers at market age
Shaojun He, Qirun Yin, Yongjie Xiong, Jing Li, Deyi Liu
Tropical Animal Health and Production.2020; 52(6): 3833. CrossRef
Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes
K.M. Feye, M.F.A. Baxter, G. Tellez-Isaias, M.H. Kogut, S.C. Ricke
Poultry Science.2020; 99(2): 653. CrossRef
Genome reconstruction of a novel carbohydrate digesting bacterium from the chicken caecal microflora
Ankit T. Hinsu, Ramesh J. Pandit, Shriram H. Patel, Androniki Psifidi, Fiona M. Tomley, Subrata K. Das, Damer P. Blake, Chaitanya G. Joshi
Meta Gene.2019; 20: 100543. CrossRef
Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review
Zenon Zduńczyk
Annals of Animal Science.2019; 19(2): 239. CrossRef
Faecalibacterium diversity in dairy cow milk
Keith W. Savin, Jody Zawadzki, Martin J. Auldist, Jianghui Wang, Doris Ram, Simone Rochfort, Benjamin G. Cocks, Christopher Staley
PLOS ONE.2019; 14(8): e0221055. CrossRef
Olfactory Communication via Microbiota: What Is Known in Birds?
Öncü Maraci, Kathrin Engel, Barbara A. Caspers
Genes.2018; 9(8): 387. CrossRef

Effect of dietary copper level on the gut microbiota and its correlation with serum inflammatory cytokines in Sprague-Dawley rats: Feng Zhang , Weijiang Zheng , Rong Guo , Wen Yao; J. Microbiol. 2017;55(9):694-702. Published online September 2, 2017; DOI: https://doi.org/10.1007/s12275-017-6627-9

377 View
0 Download
41 Crossref

Abstract PDF

In China’s swine industry, copper is generally supplemented above the National Research Council (NRC) requirement (2012) because of its antimicrobial properties and the potential for growth promotion. Yet few are concerned about whether this excess supplementation is necessary. In this study, the 16S rRNA pyrosequencing was designed and used to investigate the effect of dietary copper level on the diversity of the fecal microbial community and the correlation of copper level with the serum level of inflammatory cytokines in Sprague-Dawley rat models. The results showed that the diet containing a high level of Cu (120 and 240 mg/kg) changed the microbial richness and diversity of rat feces associated with the increased copper content in the rat ileac and colonic digesta. Furthermore, a Pearson’s correlation analysis indicated that an accumulation of unabsorbed copper in the chyme was correlated with the microbial composition of the rat feces, which was linked with TNF-α in serum. The results suggest that dietary copper level may have a direct impact on circulating inflammatory cytokines in the serum, perhaps inducing an inflammatory response by altering the microbial composition of rat feces. Serum TNF-α could be the chief responder to excessive copper exposure.

Citations

Citations to this article as recorded by

Biomarker Discovery in Wilson’s Disease—A Path Toward Improved Diagnosis and Management: A Comprehensive Review
Marta Wolska, Zofia Wicik, Sara Ahmadova, Dagmara Mirowska-Guzel, Marek Postula, Anna Czlonkowska, Ceren Eyileten
Molecular Neurobiology.2025;[Epub] CrossRef
Dietary copper to zinc ratio intake and irritable bowel syndrome risk: a large-scale prospective cohort study from UK Biobank
Yan Zhuang, Laifu Li, Yan Ran, Yanqi Zhang, Jiamiao Chen, Xuna Liu, Beibei Zeng, Boxu Zhu, Fei Dai
American Journal of Epidemiology.2025; 194(8): 2184. CrossRef
Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites
Matthew L. Klein, Christian B. Erikson, Conor J. McCabe, Laibin Huang, Jorge L. Mazza Rodrigues, Frank M. Mitloehner
Frontiers in Microbiology.2025;[Epub] CrossRef
Effect of inulin supplementation in maternal fecal microbiota transplantation on the early growth of chicks
Mengxian Chen, Junxing Pan, Yang Song, Shenao Liu, Peng Sun, Xin Zheng
Microbiome.2025;[Epub] CrossRef
Nutritional Characteristics, Health Impact, and Applications of Kefir
Oladayo Emmanuel Apalowo, Grace Adeola Adegoye, Teresia Mbogori, Jayanthi Kandiah, Tolulope Mobolaji Obuotor
Foods.2024; 13(7): 1026. CrossRef
Effects of Plant Polysaccharides Combined with Boric Acid on Digestive Function, Immune Function, Harmful Gas and Heavy Metal Contents in Faeces of Fatteners
Juan Deng, Feng Zhang, Haoran Fan, Yuxuan Zheng, Chunfang Zhao, Man Ren, Erhui Jin, Youfang Gu
Animals.2024; 14(11): 1515. CrossRef
Association between Exposure to Metals during Pregnancy, Childhood Gut Microbiome, and Risk of Intestinal Inflammation in Late Childhood
Vishal Midya, Manasi Agrawal, Jamil M. Lane, Chris Gennings, Leonid Tarassishin, Libni A. Torres-Olascoaga, Joseph Eggers, Jill K. Gregory, Mellissa Picker, Inga Peter, Jeremiah J. Faith, Manish Arora, Martha M. Téllez-Rojo, Robert O. Wright, Jean-Frederi
Environment & Health.2024; 2(10): 739. CrossRef
Arsenic induced neurotoxicity in the brain of ducks: The potential involvement of the gut-brain axis
Shaofeng Wu, Gaolong Zhong, Qian Su, Ting Hu, Gan Rao, Tong Li, Yuhan Wu, Zhiyan Ruan, Hui Zhang, Zhaoxin Tang, Lianmei Hu
Journal of Trace Elements in Medicine and Biology.2024; 81: 127336. CrossRef
Toxic and essential metals: metabolic interactions with the gut microbiota and health implications
Qinheng Zhu, Boyan Chen, Fu Zhang, Baodan Zhang, Yujie Guo, Mengtao Pang, Liang Huang, Tianjiao Wang
Frontiers in Nutrition.2024;[Epub] CrossRef
The emerging role of copper in depression
Jinhua Chen, Wenping Song, Wenzhou Zhang
Frontiers in Neuroscience.2023;[Epub] CrossRef
Disruption of intestinal structure, tight junction complex, immune response and microbiota after chronic exposure to copper in swamp eel (Monopterus albus)
Changgao Lin, Jianping Fu, Lin Liu, Hui Wang, Lili Wei
Fish & Shellfish Immunology.2023; 143: 109182. CrossRef
Effect of high-copper diet on transference of blaCTX−M genes among Escherichia coli strains in rats' intestine
Kang Liu, Linqian Li, Mengwei Weng, Feng Zhang, Rong Guo, Jinhu Huang, Wen Yao
Frontiers in Veterinary Science.2023;[Epub] CrossRef
The role of heavy metal exposure on the microbiome in the etiology of gastrointestinal disorders: a scoping review
Olga V. Delyukina, Sergey A. Savko, Elena V. Rylina, Ekaterina A. Bilous, Tatiana V. Korobeynikova, Anatoly V. Skalny
Ekologiya cheloveka (Human Ecology).2023; 30(10): 735. CrossRef
Predicting foodborne pathogens and probiotics taxa within poultry-related microbiomes using a machine learning approach
Moses B. Ayoola, Nisha Pillai, Bindu Nanduri, Michael J. Rothrock Jr, Mahalingam Ramkumar
Animal Microbiome.2023;[Epub] CrossRef
Phosphorylated Fish Gelatin and the Quality of Jelly Gels: Gelling and Microbiomics Analysis
Shiyu Wu, Wanyi Sun, Yihui Yang, Ru Jia, Shengnan Zhan, Changrong Ou, Tao Huang
Foods.2023; 12(19): 3682. CrossRef
Effects of organic and inorganic copper on cecal microbiota and short-chain fatty acids in growing rabbits
Yanan Du, Yun Tu, Zeyang Zhou, Rui Hong, Jiayou Yan, Gong-Wei Zhang
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Ionomics-metabolome association analysis as a new approach to the impact of dietary copper levels in suckling piglets model
Feng Zhang, Wen Yao, Xu Ji, Xiaodan Liu, Erhui Jin
Scientific Reports.2023;[Epub] CrossRef
Battery wastewater induces nephrotoxicity via disordering the mitochondrial dynamics
Jiangnan Yi, Jianzhao Liao, Tian Bai, Bole Wang, Chamba Yangzom, Zulfiqar Ahmed, Khalid Mehmood, Rao Zahid Abbas, Ying Li, Zhaoxin Tang, Hui Zhang
Chemosphere.2022; 303: 135018. CrossRef
Effect of Dietary Fructus mume and Scutellaria baicalensis Georgi on the Fecal Microbiota and Its Correlation with Apparent Nutrient Digestibility in Weaned Piglets
Feng Zhang, Erhui Jin, Xiaodan Liu, Xu Ji, Hong Hu
Animals.2022; 12(18): 2418. CrossRef
Latent Benefits and Toxicity Risks Transmission Chain of High Dietary Copper along the Livestock–Environment–Plant–Human Health Axis and Microbial Homeostasis: A Review
Yongkang Zhen, Ling Ge, Qiaoqing Chen, Jun Xu, Zhenyu Duan, Juan J. Loor, Mengzhi Wang
Journal of Agricultural and Food Chemistry.2022; 70(23): 6943. CrossRef
Effects of trace minerals supply from rumen sustained release boluses on milk yields and components, rumen fermentation and the rumen bacteria in lactating yaks (Bos grunniens)
Z.W. Zhao, Z.Y. Ma, H.C. Wang, C.F. Zhang
Animal Feed Science and Technology.2022; 283: 115184. CrossRef
Effect of organic and nano copper at reduced dietary levels on biochemical profile and immune response of Giriraja and Swarnadhara birds
NOOR AMINULLAH, T M PRABHU, B N SURESH, V MALATHI, MOHAMMAD DAWOOD BAWER, H M YATHISH
The Indian Journal of Animal Sciences.2022;[Epub] CrossRef
Metagenomic analysis of intestinal microbiota in wild rats living in urban and rural habitats
Rafig Gurbanov, Uygar Kabaoğlu, Tuba Yağcı
Folia Microbiologica.2022; 67(3): 469. CrossRef
How copper can impact pig growth: comparing the effect of copper sulfate and monovalent copper oxide on oxidative status, inflammation, gene abundance, and microbial modulation as potential mechanisms of action
Asal Forouzandeh, Laia Blavi, Jose Francisco Pérez, Matilde D’Angelo, Francesc González-Solé, Alessandra Monteiro, Hans H Stein, David Solà-Oriol
Journal of Animal Science.2022;[Epub] CrossRef
Gut homeostasis and microbiota under attack: impact of the different types of food contaminants on gut health
Moamen M. Elmassry, Ahmed Zayed, Mohamed A. Farag
Critical Reviews in Food Science and Nutrition.2022; 62(3): 738. CrossRef
Low-dose florfenicol and copper combined exposure during early life induced health risks by affecting gut microbiota and metabolome in SD rats
Zheng Ma, Xue Gao, Xiao Yang, Lin Lin, Xiangyi Wei, Shuhan Wang, Yuke Li, Xinyue Peng, Chuchu Zhao, Jinyao Chen, Hang Xiao, Ya Yuan, Juan Dai
Ecotoxicology and Environmental Safety.2022; 245: 114120. CrossRef
Histological alterations, oxidative stress, and inflammatory response in the liver of swamp eel (Monopterus albus) acutely exposed to copper
Lin Liu, Qiubai Zhou, Changgao Lin, Li He, Lili Wei
Fish Physiology and Biochemistry.2021; 47(6): 1865. CrossRef
Arsenic exposure induces intestinal barrier damage and consequent activation of gut-liver axis leading to inflammation and pyroptosis of liver in ducks
Gaolong Zhong, Fang Wan, Juan Lan, Xuanxuan Jiang, Shaofeng Wu, Jiaqiang Pan, Zhaoxin Tang, Lianmei Hu
Science of The Total Environment.2021; 788: 147780. CrossRef
Influence of toxic metal exposure on the gut microbiota (Review)
Federica Giambò, Sebastiano Italia, Michele Teodoro, Giusi Briguglio, Nicola Furnari, Rosaria Catanoso, Chiara Costa, Concettina Fenga
World Academy of Sciences Journal.2021;[Epub] CrossRef
Contribution of trace element exposure to gestational diabetes mellitus through disturbing the gut microbiome
Yuqing Zhang, Ting Chen, Yiyun Zhang, Qi Hu, Xu Wang, Hang Chang, Jian-Hua Mao, Antoine M. Snijders, Yankai Xia
Environment International.2021; 153: 106520. CrossRef
Recent Advances in Understanding the Influence of Zinc, Copper, and Manganese on the Gastrointestinal Environment of Pigs and Poultry
Leon J. Broom, Alessandra Monteiro, Arturo Piñon
Animals.2021; 11(5): 1276. CrossRef
Effects of dicopper oxide and copper sulfate on growth performance and gut microbiota in broilers
A. Forouzandeh, L. Blavi, N. Abdelli, D. Melo-Duran, A. Vidal, M. Rodríguez, A.N.T.R. Monteiro, J.F. Pérez, L. Darwich, D. Solà-Oriol
Poultry Science.2021; 100(8): 101224. CrossRef
Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats
Juan Dai, Xiao Yang, Ya Yuan, Youzhen Jia, Guibing Liu, Nan Lin, Hang Xiao, Lishi Zhang, Jinyao Chen
Toxicology.2020; 433-434: 152395. CrossRef
Copper induces oxidative stress with triggered NF-κB pathway leading to inflammatory responses in immune organs of chicken
Fan Yang, Jianzhao Liao, Wenlan Yu, Ruonan Pei, Na Qiao, Qingyue Han, Lianmei Hu, Ying Li, Jianying Guo, Jiaqiang Pan, Zhaoxin Tang
Ecotoxicology and Environmental Safety.2020; 200: 110715. CrossRef
Effects of trace mineral supply from rumen boluses on performance, carcass characteristics, and fecal bacterial profile in beef cattle
Chanhee Lee, Jacob E. Copelin, Phyllis A. Dieter, Elizabeth A. Berry
Animal Feed Science and Technology.2020; 269: 114626. CrossRef
Dietary manganese requirement and its effects on antioxidant enzyme activities, intestinal morphology and microbiota in oriental river prawn Macrobrachium nipponense (De Haan)
Zhili Ding, Xuefeng Chen, Youqin Kong, Xianping Shao, Yixiang Zhang, Jinyun Ye
Aquaculture.2020; 516: 734622. CrossRef
Effects of mineral methionine hydroxy analog chelate in sow diets on epigenetic modification and growth of progeny
Ki Beom Jang, Jong Hyuk Kim, Jerry M Purvis, Juxing Chen, Ping Ren, Mercedes Vazquez-Anon, Sung Woo Kim
Journal of Animal Science.2020;[Epub] CrossRef
Advances in the mechanism of high copper diets in restraining pigs growth
Yang Gao, Wenyan Yang, Dongsheng Che, Seidu Adams, Lianyu Yang
Journal of Animal Physiology and Animal Nutrition.2020; 104(2): 667. CrossRef
Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels
Feng Zhang, Weijiang Zheng, Yongqiang Xue, Wen Yao
Applied Microbiology and Biotechnology.2019; 103(2): 853. CrossRef
Copper bioavailability, mineral utilization, and lipid metabolism in broilers
Aiyou Wen, Sifa Dai, Xuezhuang Wu, Zhihua Cai
Czech Journal of Animal Science.2019; 64(12): 483. CrossRef
Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions
John Tsiaoussis, Michael N. Antoniou, Ioannis Koliarakis, Robin Mesnage, Constantine I. Vardavas, Boris N. Izotov, Anna Psaroulaki, Aristidis Tsatsakis
Toxicology Letters.2019; 312: 72. CrossRef

Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant: Young Ki Hahn , Minseok S. Kim , Wan-Taek Im; J. Microbiol. 2017;55(8):607-611. Published online July 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7257-y

329 View
0 Download
4 Crossref

Abstract PDF

A Gram negative, aerobic, non-motile and rod-shaped bacterial strain designated as Gr-2T was isolated from granules used in a wastewater treatment plant in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain Gr-2T grew at 18–37°C (optimum temperature, 30°C) and a pH of 6.0–8.0 (optimum pH, 7.0) on R2A agar medium. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Pseudaminobacter of the family Phyllobacteriaceae, and formed clusters with Pseudaminobacter defluvii THI 051T (98.9%) and Pseudaminobacter salicylatoxidans BN12T (98.7%). The G+C content of the genomic DNA was 63.6%. The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major fatty acids were cyclo-C19:0 ω8c, C18:1 ω7c, and iso-C17:0. The overall polar lipid patterns of Gr-2T were similar to those determined for the other Pseudaminobacter species. DNA-DNA relatedness values between strain Gr-2T and its closest phylogenetically neighbors were below 18%. Strain Gr-2T could be differentiated genotypically and phenotypically from the recognized species of the genus Pseudaminobacter. The isolate therefore represents a novel species, for which the name Pseudaminobacter granuli sp. nov. is proposed with the type strain Gr-2T (=KACC 18877T =LMG 29567T).

Citations

Citations to this article as recorded by

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications
Saqlain Mustaq, Abdul Moin, Baishali Pandit, Bipransh Kumar Tiwary, Masrure Alam
Folia Microbiologica.2024; 69(1): 17. CrossRef
Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species
Yan Li, Tingyan Guo, Liqin Sun, En-Tao Wang, J. Peter W. Young, Chang-Fu Tian
BMC Genomics.2024;[Epub] CrossRef
Degradation of neonicotinoid insecticide acetamiprid by two different nitrile hydratases of Pseudaminobacter salicylatoxidans CGMCC 1.17248
Leilei Guo, Wenlong Yang, Xi Cheng, Zhixia Fan, Ximeng Chen, Feng Ge, Yijun Dai
International Biodeterioration & Biodegradation.2021; 157: 105141. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain: Qingmei Liu , Muhammad Zubair Siddiqi , Mi-Sun Kim , Sang Yong Kim , Wan-Taek Im; J. Microbiol. 2017;55(7):525-530. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-7180-2

299 View
0 Download
6 Crossref

Abstract PDF

A Gram-negative, non-motile, aerobic, and rod-shaped bacterial strain designated as BR5-28T was isolated from the soil of a ginseng field at Baekdu Mountain Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BR5-28T grew at 10–42°C (optimum temperature, 30°C) and pH 5.5–8.5 (optimum pH, 7.0) on R2A agar medium without additional NaCl supplementation. Strain BR5- 28T exhibited β-glucosidase activity, which was responsible for its ability to transform the ginsenosides Rb1 and Rd (the two dominant active components of ginseng) to compound-K. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Mucilaginibacter of the family Sphingobacteriaceae, and formed clusters with Mucilaginibacter frigoritolerans FT22T (95.8%) and Mucilaginibacter gotjawali SA3-7T (95.7%). The G+C content of the genomic DNA was 45.1%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c), iso-C15:0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain BR5- 28T was differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter hankyongensis sp. nov. is proposed, with the type strain BR5-28T (=KCTC 22274T =DSM 21151T).

Citations

Citations to this article as recorded by

Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter
Jiyoun Kim, Byungjo Lee, Geeta Chhetri, Inhyup Kim, Yoonseop So, Wonhee Jang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Biologically facilitated precipitation of metals in low-Fe waters at the sulphidic Mount Chalmers mine, Queensland, Australia
Anicia Henne, Dave Craw, Emma Gagen, Gordon Southam
Ore Geology Reviews.2021; 136: 104238. CrossRef
Mucilaginibacter hurinus sp. nov., isolated from briquette warehouse soil
Lina Choi, Xinran Zhao, Yali Song, Minghan Wu, Gejiao Wang, Mingshun Li
Archives of Microbiology.2020; 202(1): 127. CrossRef
Mucilaginibacter panaciglaebae sp. nov., isolated from soil of a ginseng field
Soon Youl Lee, Muhammad Zubair Siddiqi, Sang Yong Kim, Hong Shan Yu, Jae Hak Lee, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 149. CrossRef
Terrabacter ginsengisoli sp. nov., isolated from ginseng cultivating soil
Mei-Fang Jin, Xiao-Tian Quan, Muhammad Zubair Siddiqi, Qing-Zhen Liu, Hong-Shan Yu, Wan-Taek Im
Journal of Microbiology.2018; 56(5): 331. CrossRef
Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine
Yuan Ping Li, Nicolas Carraro, Nan Yang, Bixiu Liu, Xian Xia, Renwei Feng, Quaiser Saquib, Hend A Al-Wathnani, Jan Roelof Van der Meer, Christopher Rensing
Genes.2018; 9(12): 573. CrossRef

Exploring the oral microflora of preschool children: Wen Ren , Qun Zhang , Xuenan Liu , Shuguo Zheng , Lili Ma , Feng Chen , Tao Xu , Baohua Xu; J. Microbiol. 2017;55(7):531-537. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-6474-8

335 View
1 Download
23 Crossref

Abstract PDF

The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences. We found the highest α diversity, microbial richness, and evenness in plaque, compared with saliva and tongue coating. Plaque was also distinguished from saliva and tongue coating by phylogenetic distances (weighted UniFrac). Taxa with different relative abundances were further identified, confirming the existence of microbial differences across the three niches. Core microbiomes were defined of each niche; however, only a small proportion of operational taxonomic units (8.07%) were shared by the three niches. Coaggregation between Actinomyces spp. and Streptococcus spp. and other correlations among periodontal pathogens, such as Prevotella, Fusobacteria, Capnocytophaga, and Tannerella, were shown by a co-occurrence network. In summary, our study provides a framework of oral microbial communities in the population of preschool children as a baseline for further studies of oral diseases related to microbes.

Citations

Citations to this article as recorded by

Salivary microbiota dysbiosis and elevated polyamine levels contribute to the severity of periodontal disease
Md Haroon Rashid, Sandhya Pavan Kumar, Resma Rajan, Anitha Mamillapalli
BMC Oral Health.2025;[Epub] CrossRef
A dynamic microcosm biofilm model for root carious-like lesion development: analysis of demineralization and microbiological characterization
Tamires Timm Maske, Glenda Ávila Marques, Bruna Dalongaro Fritsch, Bruna Moraes Kremer, Maximiliano Sérgio Cenci, Pabulo Henrique Rampelotto, Rodrigo Alex Arthur
Biofouling.2025; 41(5): 536. CrossRef
Oral microbiota analysis of tongue coating in patients with esophageal adenocarcinoma
Huijie Wang, Jinfeng Wang, Jinli Liu, Xiaoyang Shi, Zhichao Wang, Xu Cao
Medicine.2025; 104(41): e45160. CrossRef
The Infant Oral Microbiome: Developmental Dynamics, Modulating Factors, and Implications for Oral and Systemic Health
Paula Olate, Ailín Martínez, Eulàlia Sans-Serramitjana, Matías Cortés, Rommy Díaz, Genisley Hernández, Erwin A. Paz, Néstor Sepúlveda, John Quiñones
International Journal of Molecular Sciences.2025; 26(16): 7983. CrossRef
The tongue microbiome of young patients with chronic kidney disease and their healthy mothers
Karolin C. Hoefer, Lutz T. Weber, Anna Greta Barbe, Isabelle Graf, Stefanie Thom, Angela Nowag, Claus J. Scholz, Hilmar Wisplinghoff, Michael J. Noack, Nathalie Jazmati
Clinical Oral Investigations.2024;[Epub] CrossRef
Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs
Giulia Alessandri, Federico Fontana, Leonardo Mancabelli, Chiara Tarracchini, Gabriele Andrea Lugli, Chiara Argentini, Giulia Longhi, Sonia Mirjam Rizzo, Laura Maria Vergna, Rosaria Anzalone, Alice Viappiani, Francesca Turroni, Maria Cristina Ossiprandi,
FEMS Microbiology Ecology.2024;[Epub] CrossRef
Molecular Genetic Analysis of Perioperative Colonization by Infection-Related Microorganisms in Patients Receiving Intraoral Microvascular Grafts
Henriette Louise Moellmann, Katharina Kommer, Nadia Karnatz, Klaus Pfeffer, Birgit Henrich, Majeed Rana
Journal of Clinical Medicine.2024; 13(14): 4103. CrossRef
Advances in the oral microbiota and rapid detection of oral infectious diseases
Xuan Xiao, Shangfeng Liu, Hua Deng, Yuhan Song, Liang Zhang, Zhifeng Song
Frontiers in Microbiology.2023;[Epub] CrossRef
Novel Strategies for Preventing Dysbiosis in the Oral Cavity
Mariana B Rebelo, Cláudia S Oliveira, Freni K Tavaria
Frontiers in Bioscience-Elite.2023;[Epub] CrossRef
Lactobacillus paracasei ET-22 Suppresses Dental Caries by Regulating Microbiota of Dental Plaques and Inhibiting Biofilm Formation
Meng Guo, Jianmin Wu, Weilian Hung, Zhe Sun, Wen Zhao, Hanglian Lan, Zhi Zhao, Guna Wuri, Bing Fang, Liang Zhao, Ming Zhang
Nutrients.2023; 15(15): 3316. CrossRef
Exploring Oral Microbiome in Healthy Infants and Children: A Systematic Review
Silvia D’Agostino, Elisabetta Ferrara, Giulia Valentini, Sorana Andreea Stoica, Marco Dolci
International Journal of Environmental Research and Public Health.2022; 19(18): 11403. CrossRef
Sonication versus the conventional method for evaluation of the dental microbiome: a prospective pilot study
Oliver Wagendorf, Peter Menzel, Rolf Schwarzer, Norbert Neckel, Saskia Preissner, Max Heiland, Susanne Nahles
BMC Oral Health.2022;[Epub] CrossRef
The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions
Xinyi Li, Yanmei Liu, Xingyou Yang, Chengwen Li, Zhangyong Song
Frontiers in Microbiology.2022;[Epub] CrossRef
Predominance of non-Streptococcus mutans bacteria in dental biofilm and its relation to caries progression
Doaa M. AlEraky, Marwa Madi, Maha El Tantawi, Jehan AlHumaid, Sarah Fita, Sayed AbdulAzeez, J. Francis Borgio, Fahad A. Al-Harbi, Adel S. Alagl
Saudi Journal of Biological Sciences.2021; 28(12): 7390. CrossRef
The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey
Xiaoxia Yang, Lidan He, Siqi Yan, Xinyi Chen, Guoying Que
BMC Oral Health.2021;[Epub] CrossRef
Acquisition and establishment of the oral microbiota
A. M. (Marije) Kaan, Dono Kahharova, Egija Zaura, M. Curtis, R. Darveau
Periodontology 2000.2021; 86(1): 123. CrossRef
Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience
Eungyung Lee, Suhyun Park, Sunwoo Um, Seunghoon Kim, Jaewoong Lee, Jinho Jang, Hyoung-oh Jeong, Jonghyun Shin, Jihoon Kang, Semin Lee, Taesung Jeong
Diagnostics.2021; 11(8): 1324. CrossRef
Relationship of Salivary Microbiome with the Worsening of the Periodontal Health Status in Young Adults: A 3-Year Cohort Study
Md Monirul Islam, Daisuke Ekuni, Naoki Toyama, Terumasa Kobayashi, Kohei Fujimori, Yoko Uchida, Daiki Fukuhara, Ayano Taniguchi-Tabata, Kota Kataoka, Yoshiaki Iwasaki, Manabu Morita
International Journal of Environmental Research and Public Health.2020; 17(5): 1764. CrossRef
The canine oral microbiome: variation in bacterial populations across different niches
Avika Ruparell, Taichi Inui, Ruth Staunton, Corrin Wallis, Oliver Deusch, Lucy J. Holcombe
BMC Microbiology.2020;[Epub] CrossRef
The oral microbiome and salivary proteins influence caries in children aged 6 to 8 years
Wang Chen, Qian Jiang, Guowei Yan, Deqin Yang
BMC Oral Health.2020;[Epub] CrossRef
MEDICAL AND GENETIC STUDIES OF ORAL MICROBIOMA STATUS IN CHILDREN
S. S. Ostrovska, P. G. Gerasimchuk
Bulletin of Problems Biology and Medicine.2019; 4(1): 43. CrossRef
The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human
Anthony P. Corfield
Microorganisms.2018; 6(3): 78. CrossRef
Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth
Weihua Shi, Jing Tian, He Xu, Qiong Zhou, Man Qin, Kazuhiro Takemoto
PLOS ONE.2018; 13(7): e0200337. CrossRef

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices: Jae-Hyung Ahn , Shin Ae Lee , Jeong Myeong Kim , Myung-Sook Kim , Jaekyeong Song , Hang-Yeon Weon; J. Microbiol. 2016;54(11):724-731. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6463-3

331 View
0 Download
28 Crossref

Abstract PDF

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.

Citations

Citations to this article as recorded by

Straw return enhances the global warming potential in paddy soil under the regulation of functional genes
Ziying Cui, Jingli Wei, Yukun Pan, Wen Zhang, Jialong Lv, Yajun Yang
Environmental Technology & Innovation.2025; 39: 104293. CrossRef
Ramifications of crop residue loading for soil microbial community composition, activity and nutrient supply
Newton Z. Lupwayi, Benjamin H. Ellert, Eric Bremer, Elwin G. Smith, Renee M. Petri, Jonathan A. D. Neilson, H. Henry Janzen
Soil Use and Management.2023; 39(1): 402. CrossRef
Three decades of organic manure and chemical fertilizers co-application enhanced rice productivity through increasing the diversity and key network module of soil bacterial community
Xiran Zhao, Jun Li, Xin Hu, Baowei Hu, Guixin Chu, Rui Tao
Journal of Soils and Sediments.2023; 23(5): 2175. CrossRef
A 40 % paddy surface soil organic carbon increase after 5-year no-tillage is linked with shifts in soil bacterial composition and functions
Jian-Ying Qi, Xiang-Bin Yao, Jian Lu, Long-Xin He, Jun-Li Cao, Zheng-Rong Kan, Xing Wang, Sheng-Gang Pan, Xiang-Ru Tang
Science of The Total Environment.2023; 859: 160206. CrossRef
Bacterial community of agricultural soils used for potato cultivation in Sverdlovsk region
E. P. Shanina, G. A. Lihodeevskiy
Agricultural Science Euro-North-East.2023; 24(6): 989. CrossRef
Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks
Ruifen Zhu, Chang Liu, Yuan Dong Xu, Wei He, Jielin Liu, Jishan Chen, Yajun An, Shangli Shi
Frontiers in Microbiology.2022;[Epub] CrossRef
The effect of environmental parameters and fertilization practices on yield and soil microbial diversity in a Kenyan paddy rice field
Markus Gorfer, Luigimaria Borruso, Evi Deltedesco, Emily W. Gichuhi, Daniel M. Menge, Daigo Makihara, Nadine Praeg, Stefano Cesco, Tanja Mimmo, Lutz Merbold, Sonja Leitner
Applied Soil Ecology.2022; 176: 104495. CrossRef
Bacterial Diversity and Potential Functions in Response to Long-Term Nitrogen Fertilizer on the Semiarid Loess Plateau
Aixia Xu, Lingling Li, Junhong Xie, Renzhi Zhang, Zhuzhu Luo, Liqun Cai, Chang Liu, Linlin Wang, Sumera Anwar, Yuji Jiang
Microorganisms.2022; 10(8): 1579. CrossRef
Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction
Hong-Yi Li, Hang Wang, Xin-Hua Tao, Xian-Zhe Wang, Wei-Zheng Jin, Jack A. Gilbert, Yong-Guan Zhu, Zhi-Jian Zhang, Elizabeth Anne Shank
mSystems.2021;[Epub] CrossRef
Methanogenesis and Methane Oxidation in Paddy Fields under Organic Fertilization
Chungwoo Kim, Denver I. Walitang, Tongmin Sa
Korean Journal of Environmental Agriculture.2021; 40(4): 295. CrossRef
Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India
Pranamita Kunda, Abhishek Mukherjee, Paltu Kumar Dhal
World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef
Response of root nutrient resorption strategies to rhizosphere soil microbial nutrient utilization along Robinia pseudoacacia plantation chronosequence
Miaoping Xu, Junnan Jian, Jiayi Wang, Zhenjiao Zhang, Gaihe Yang, Xinhui Han, Chengjie Ren
Forest Ecology and Management.2021; 489: 119053. CrossRef
Organic Manure Management Increases Soil Microbial Community Structure and Diversity in the Double-cropping Rice Paddy Field of Southern China
Chao Li, Lihong Shi, Haiming Tang, Kaikai Cheng, Li Wen, Weiyan Li, Xiaoping Xiao, Ke Wang
Communications in Soil Science and Plant Analysis.2021; 52(11): 1224. CrossRef
Soil microbial communities in tilled organic and no-till conventional crop production systems
Newton Z. Lupwayi, Cynthia A. Grant, John T. O’Donovan, Andrea H. Eastman, Greg Semach, Derrick A. Kanashiro, Renee M. Petri
Organic Agriculture.2021; 11(4): 553. CrossRef
Profiles of wheat rhizobacterial communities in response to repeated glyphosate applications, crop rotation, and tillage
Newton Z. Lupwayi, Myriam R. Fernandez, Derrick A. Kanashiro, Renee M. Petri, M. Anne Naeth
Canadian Journal of Soil Science.2021; 101(1): 157. CrossRef
Fifteen-year no tillage of a Mollisol with residue retention indirectly affects topsoil bacterial community by altering soil properties
Meng Li, Peng He, Xiao-Li Guo, Xingyi Zhang, Lu-Jun Li
Soil and Tillage Research.2021; 205: 104804. CrossRef
Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China
Xiaoqin Yang, Yang Wang, Luying Sun, Xiaoning Qi, Fengbin Song, Xiancan Zhu
Agronomy.2020; 10(10): 1526. CrossRef
Long-term effects of vegetation and soil on the microbial communities following afforestation of farmland with Robinia pseudoacacia plantations
Miaoping Xu, Dexin Gao, Shuyue Fu, Xuqiao Lu, Shaojun Wu, Xinhui Han, Gaihe Yang, Yongzhong Feng
Geoderma.2020; 367: 114263. CrossRef
Effects of short-term manure nitrogen input on soil microbial community structure and diversity in a double-cropping paddy field of southern China
Haiming Tang, Chao Li, Xiaoping Xiao, Lihong Shi, Kaikai Cheng, Li Wen, Weiyan Li
Scientific Reports.2020;[Epub] CrossRef
Different types of agricultural land use drive distinct soil bacterial communities
Shin Ae Lee, Jeong Myeong Kim, Yiseul Kim, Jae-Ho Joa, Seong-Soo Kang, Jae-Hyung Ahn, Mincheol Kim, Jaekyeong Song, Hang-Yeon Weon
Scientific Reports.2020;[Epub] CrossRef
Effects of long‐term fertilizer management on soil bacterial diversity in double‐cropping paddy field of southern China
Haiming Tang, Yilan Xu, Chao Li, Xiaoping Xiao, Kaikai Cheng, Lihong Shi, Xiaochen Pan, Weiyan Li, Li Wen
Agronomy Journal.2020; 112(5): 3644. CrossRef
Long-term phosphorus limitation changes the bacterial community structure and functioning in paddy soils
Sandipan Samaddar, Poulami Chatterjee, Jaak Truu, Rangasamy Anandham, Sukjin Kim, Tongmin Sa
Applied Soil Ecology.2019; 134: 111. CrossRef
Long-term silicate fertilization increases the abundance of Actinobacterial population in paddy soils
Sandipan Samaddar, Jaak Truu, Poulami Chatterjee, Marika Truu, Kiyoon Kim, Sukjin Kim, Sundaram Seshadri, Tongmin Sa
Biology and Fertility of Soils.2019; 55(2): 109. CrossRef
The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea
Sherlyn C. Tipayno, Jaak Truu, Sandipan Samaddar, Marika Truu, Jens‐Konrad Preem, Kristjan Oopkaup, Mikk Espenberg, Poulami Chatterjee, Yeongyeong Kang, Kiyoon Kim, Tongmin Sa
Ecology and Evolution.2018; 8(12): 6157. CrossRef
Soil bacterial community responses to black medic cover crop and fertilizer N under no-till
Newton Z. Lupwayi, William E. May, Derrick A. Kanashiro, Renee M. Petri
Applied Soil Ecology.2018; 124: 95. CrossRef
Aquatic plant debris changes sediment enzymatic activity and microbial community structure
Wan-Lei Xue, Wei Pan, Qi Lu, Qian-Ru Xu, Cai-Nan Wu, Shao-Ting Du
Environmental Science and Pollution Research.2018; 25(22): 21801. CrossRef
Soil microbial community and activity are affected by integrated agricultural practices in China
X. C. Zhu, L. Y. Sun, F. B. Song, S. Q. Liu, F. L. Liu, X. N. Li
European Journal of Soil Science.2018; 69(5): 924. CrossRef
Pyrosequencing reveals profiles of soil bacterial communities after 12 years of conservation management on irrigated crop rotations
Newton Z. Lupwayi, Francis J. Larney, Robert E. Blackshaw, Derrick A. Kanashiro, Drusilla C. Pearson, Renee M. Petri
Applied Soil Ecology.2017; 121: 65. CrossRef

Research Support, Non-U.S. Gov'ts

Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing: Da-Eun Lee , Jinhwan Lee , Young-Mog Kim , Jeong-In Myeong , Kyoung-Ho Kim; J. Microbiol. 2016;54(4):296-304. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5571-4

358 View
0 Download
31 Crossref

Abstract PDF

Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

Citations

Citations to this article as recorded by

Effects of Feeding Frequency on Turbot (Scophthalmus maximus) Performance, Water Quality and Microbial Community in Recirculating Aquaculture Systems
Xiaoyang Guo, Jiyuan Li, Shihong Xu, Xin Jiang, Teng Guo, Feng Liu, Guang Gao, Jun Li, Yanfeng Wang, Wei Jiang
Fishes.2025; 10(3): 125. CrossRef
Bacterial community in African catfish (Clarias gariepinus) recirculating aquaculture systems under different stocking densities
Júlia Clols-Fuentes, Julien A. Nguinkal, Patrick Unger, Bernd Kreikemeyer, Harry W. Palm
Frontiers in Marine Science.2023;[Epub] CrossRef
Effects of Dietary Bacillus licheniformis and Combined Herbs Extracts Supplementation on Physiological and Immune Characteristics, Microbial Community, and Vibriosis Resistance of Apostichopus japonicus
Xuda Wang, Shilei Li, Ying Dong, Rui Mi, Jingwei Jiang, Xiaoyan Guan, Bo Ye, Guiying Liu, Zhenjun Zhao, Danni Liu, Zhong Chen, Xuewen Gao, Chenyu Zhang, Zunchun Zhou, Liqiao Chen
Aquaculture Research.2023; 2023: 1. CrossRef
A Review of Bubble Aeration in Biofilter to Reduce Total Ammonia Nitrogen of Recirculating Aquaculture System
Putu Ayustin Suriasni, Ferry Faizal, Camellia Panatarani, Wawan Hermawan, I Made Joni
Water.2023; 15(4): 808. CrossRef
Seasonal Dynamics of Marine Bacterial Communities in Aquaculture Farms: The case of the Northern Ionian Coastal Ecosystem (Mediterranean Sea)
Maria Kyritsi, Antiopi Tsoureki, Konstantinos Koukaras, Nikolaos Kamidis, Grigorios Krey, Sofia Michailidou, Anagnostis Argiriou
Journal of Marine Science and Engineering.2023; 11(7): 1332. CrossRef
Seasonal and Spatial Variations of Bacterial Community Structure in the Bailang River Estuary
Wenxun Dong, Zhengguo Cui, Mengjuan Zhao, Junfeng Li
Journal of Marine Science and Engineering.2023; 11(4): 825. CrossRef
Microalgae simultaneously promote antibiotic removal and antibiotic resistance genes/bacteria attenuation in algal-bacterial granular sludge system
Wenhao Liu, Wenli Huang, Zhenhua Cao, Yuan Ji, Dongfang Liu, Weiwei Huang, Yanjing Zhu, Zhongfang Lei
Journal of Hazardous Materials.2022; 438: 129286. CrossRef
Abundance and Diversity of Nitrifying Microorganisms in Marine Recirculating Aquaculture Systems
Qintong Li, Ryo Hasezawa, Riho Saito, Kunihiro Okano, Kazuya Shimizu, Motoo Utsumi
Water.2022; 14(17): 2744. CrossRef
Dynamic changes in the microbial community in the surface seawater of Jiaozhou Bay after crude oil spills: An in situ microcosm study
Yumiao Zhou, Qiang Kong, Xinyu Zhao, Zhihao Lin, Huanxin Zhang
Environmental Pollution.2022; 307: 119496. CrossRef
Endosymbiotic microbes from entomopathogenic nematode (EPNs) and their applications as biocontrol agents for agro-environmental sustainability
Preety Tomar, Neelam Thakur, Ajar Nath Yadav
Egyptian Journal of Biological Pest Control.2022;[Epub] CrossRef
Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae
Jeeeun Park, Young-Sam Kim, Seong-Jin Kim, Sang-Eon Kim, Hyun-Kyoung Jung, Min-Ju Yu, Young Jae Jeon, Kyoung-Ho Kim
Journal of Microbiology.2021; 59(6): 546. CrossRef
Temporal dynamics of bacterial communities in the water and sediments of sea cucumber (Apostichopus japonicus) culture ponds
Zelong Zhao, Jingwei Jiang, Yongjia Pan, Ying Dong, Zhong Chen, Gaohua Zhang, Shan Gao, Hongjuan Sun, Xiaoyan Guan, Bai Wang, Yao Xiao, Zunchun Zhou
Aquaculture.2020; 528: 735498. CrossRef
Pukyongia salina gen. nov., sp. nov., a novel genus in the family Flavobacteriaceae
Young-Sam Kim, Seong-Jin Kim, Yeon Hee Jang, Kyoung-Ho Kim
Journal of Microbiology.2020; 58(6): 456. CrossRef
Integration of Marine Macroalgae (Chaetomorpha maxima) with a Moving Bed Bioreactor for Nutrient Removal from Maricultural Wastewater
Xian Li, Yale Deng, Xueying Li, Xiaona Ma, Jinxia Wang, Jun Li
Archaea.2020; 2020: 1. CrossRef
Nitrogen Removal Characteristics in a Biofilm System for Recirculating Aquaculture Wastewater Treatment under High-Salinity Conditions and Oligotrophic Stress
Lijuan Feng, Yuqin Luo, Jingyi Yang, Jingya Sun
Journal of Environmental Engineering.2020;[Epub] CrossRef
Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters
Jennifer Hüpeden, Bernd Wemheuer, Daniela Indenbirken, Carsten Schulz, Eva Spieck
Aquacultural Engineering.2020; 90: 102094. CrossRef
Characteristics of Ammonia Removal and Nitrifying Microbial Communities in a Hybrid Biofloc-RAS for Intensive Litopenaeus vannamei Culture: A Pilot-Scale Study
Wujie Xu, Yu Xu, Haochang Su, Xiaojuan Hu, Keng Yang, Guoliang Wen, Yucheng Cao
Water.2020; 12(11): 3000. CrossRef
Improved health and better survival of farmed lumpfish (Cyclopterus lumpus) after a probiotic bath with two probiotic strains of Aliivibrio
Øystein Klakegg, Siri Myhren, Rosemary Alice Juell, Marit Aase, Kira Salonius, Henning Sørum
Aquaculture.2020; 518: 734810. CrossRef
Microbial valorization of solid wastes from a recirculating aquaculture system and the relevant microbial functions
Jinhwan Lee, In-Soo Kim, Aalfin Emmanuel, Sung-Cheol Koh
Aquacultural Engineering.2019; 87: 102016. CrossRef
Tilapia recirculating aquaculture systems as a source of plant growth promoting bacteria
Francia A. Sanchez, Valerie R. Vivian‐Rogers, Hidetoshi Urakawa
Aquaculture Research.2019; 50(8): 2054. CrossRef
Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities
John I. Miller, Stephen Techtmann, Julian Fortney, Nagissa Mahmoudi, Dominique Joyner, Jiang Liu, Scott Olesen, Eric Alm, Adolfo Fernandez, Piero Gardinali, Nargiz GaraJayeva, Faig S. Askerov, Terry C. Hazen
Frontiers in Microbiology.2019;[Epub] CrossRef
Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei)
Zhao Chen, Zhiqiang Chang, Long Zhang, Yuli Jiang, Hongxing Ge, Xiefa Song, Shibo Chen, Fazhen Zhao, Jian Li
BMC Microbiology.2019;[Epub] CrossRef
Addition of commercial probiotic in a biofloc shrimp farm of Litopenaeus vannamei during the nursery phase: Effect on bacterial diversity using massive sequencing 16S rRNA
José Alberto Huerta-Rábago, Marcel Martínez-Porchas, Anselmo Miranda-Baeza, Mario Nieves-Soto, Martha Elisa Rivas-Vega, Luis Rafael Martínez-Córdova
Aquaculture.2019; 502: 391. CrossRef
Enhanced nitrate reduction in water by a combined bio-electrochemical system of microbial fuel cells and submerged aquatic plant Ceratophyllum demersum
Peng Xu, Enrong Xiao, Junmei Wu, Feng He, Yi Zhang, Zhenbin Wu
Journal of Environmental Sciences.2019; 78: 338. CrossRef
Bacterial community composition in a polyculture system ofRhopilema esculenta,Penaeus monodonandRuditapes philippinarum
Zelong Zhao, Xiaoyan Guan, Bai Wang, Ying Dong, Zunchun Zhou
Aquaculture Research.2019; 50(3): 973. CrossRef
Salaquimonas pukyongi gen. nov., sp. nov., a novel bacterium within the family Phyllobacteriaceae
Young-Sam Kim, Young Jae Jeon, Kyoung-Ho Kim
International Journal of Systematic and Evolutionary Microbiology .2019; 69(12): 3751. CrossRef
Effects of abrupt salinity increase on nitrification processes in a freshwater moving bed biofilter
John Peter Hewa Kinyage, Per Bovbjerg Pedersen, Lars-Flemming Pedersen
Aquacultural Engineering.2019; 84: 91. CrossRef
Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system
Zhitao Huang, Yuli Jiang, Xiefa Song, Eric Hallerman, Lei Peng, Dengpan Dong, Teng Ma, Jieming Zhai, Wensheng Li
AMB Express.2018;[Epub] CrossRef
Internal nitrogen removal from sediments by the hybrid system of microbial fuel cells and submerged aquatic plants
Peng Xu, En-Rong Xiao, Dan Xu, Yin Zhou, Feng He, Bi-Yun Liu, Lei Zeng, Zhen-Bin Wu, Andrew C Singer
PLOS ONE.2017; 12(2): e0172757. CrossRef
Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira
Ryan P. Bartelme, Sandra L. McLellan, Ryan J. Newton
Frontiers in Microbiology.2017;[Epub] CrossRef
Longterm Monitoring of Nitrification and Nitrifying Communities during Biofilter Activation of Two Marine Recirculation Aquaculture Systems (RAS)
Spieck Eva
International Journal of Aquaculture and Fishery Sciences.2017; : 051. CrossRef

Niabella ginsenosidivorans sp. nov., isolated from compost: Kwon-Jung Yi , Wan-Taek Im , Dong-Woon Kim , Qing Mei Liu , Soo-Ki Kim; J. Microbiol. 2015;53(11):762-766. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5463-z

310 View
0 Download
5 Crossref

Abstract

A Gram-reaction negative, strictly aerobic, non-motile, orange colored, and rod-shaped bacterium (designated BS26T) isolated from compost, was characterized by a polyphasic approach to clarify its taxonomic position. Strain BS26T was observed to grow optimally at 25–30°C and at pH 7.0 on R2A and nutrient media. Strain BS26T showed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the active components of ginseng) to ginsenoside compound-K (C-K). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BS26T belongs to the genus Niabella of family Chitinophagaceae and was most closely related to Niabella soli DSM 19437T (94.5% similarity), N. yanshanensis CCBAU 05354T (94.3%), and N. aurantiaca DSM 17617T (93.8%). The G+C content of genomic DNA was 47.3 mol%. Chemotaxonomic data [predominant isoprenoid quinone-MK-7, major fatty acids–iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c)] supported the affiliation of strain BS26T to the genus Niabella. However, strain BS26T could be differentiated genotypically and phenotypically from the recognized species of the genus Niabella. The novel isolate therefore represents a novel species, for which the name Niabella ginsenosidivorans sp. nov. is proposed, with the type strain BS26T (=KACC 16620T =JCM 18199T).

Citations

Citations to this article as recorded by

Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System
Ling Zhang, Chuansheng Geng, Xingjuan Chen, Letian Chen, Tongchu Deng, Meiying Xu
Current Microbiology.2024;[Epub] CrossRef
Niabella beijingensis sp. nov. and Thermomonas beijingensis sp. nov., two bacteria from constructed wetland
Sheng-Zhi Guo, Tong Wu, Hai-Zhen Zhu, Lei Yan, Zhi-Pei Liu, De-Feng Li, Cheng-Ying Jiang, Shuang-Jiang Liu, Xi-Hui Shen
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef
Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden
Hien T. T. Ngo, Huan Trinh, Zheng-Fei Yan, Gabriela Moya, MooChang Kook, Tae-Hoo Yi
International Journal of Systematic and Evolutionary Microbiology.2017; 67(4): 784. CrossRef
Niabella aquatica sp. nov., isolated from lake water
Muhammad Zubair Siddiqi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2016; 66(8): 2774. CrossRef

Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica: Ying-wu Shi , Kai Lou , Chun Li , Lei Wang , Zhen-yong Zhao , Shuai Zhao , Chang-yan Tian; J. Microbiol. 2015;53(10):678-685. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5080-x

323 View
0 Download
34 Crossref

Abstract

We used Illumina-based 16S rRNA V3 amplicon pyrosequencing to investigate the community structure of soil bacteria from the rhizosphere surrounding Salicornia europaea, and endophytic bacteria living in Salicornia europaea plants and Sueada aralocaspica seeds growing at the Fukang Desert Ecosystem Observation and Experimental Station (FDEOES) in Xinjiang Province, China, using an Illumina genome analyzer. A total of 89.23 M effective sequences of the 16S rRNA gene V3 region were obtained from the two halophyte species. These sequences revealed a number of operational taxonomic units (OTUs) in the halophytes. There were between 22–2,206 OTUs in the halophyte plant sample, at the 3% cutoff level, and a sequencing depth of 30,000 sequences. We identified 25 different phyla, 39 classes and 141 genera from the resulting 134,435 sequences. The most dominant phylum in all the samples was Proteobacteria (41.61%–99.26%; average, 43.30%). The other large phyla were Firmicutes (0%– 7.19%; average, 1.15%), Bacteroidetes (0%–1.64%; average, 0.44%) and Actinobacteria (0%–0.46%; average, 0.24%). This
result
suggested that the diversity of bacteria is abundant in the rhizosphere soil, while the diversity of bacteria was poor within Salicornia europaea plant samples. To the extent of our knowledge, this study is the first to characterize and compare the endophytic bacteria found within different halophytic plant species roots using PCR-based Illumina pyrosequencing
method
.

Citations

Citations to this article as recorded by

Plant Growth‐Promoting Bacteria Associated With Some Salt‐Tolerant Plants
Fatemeh Beitsayahi, Naeimeh Enayatizamir, Leila Nejadsadeghi, Fatemeh Nasernakhaei
Journal of Basic Microbiology.2024;[Epub] CrossRef
Insight into endophytic microbial diversity in two halophytes and plant beneficial attributes of Bacillus swezeyi
Lei Gao, Jin-Biao Ma, Yin Huang, Murad Muhammad, Hai-Ting Lian, Vyacheslav Shurigin, Dilfuza Egamberdieva, Wen-Jun Li, Li Li
Frontiers in Microbiology.2024;[Epub] CrossRef
Soil bacterial diversity and community structure of Suaeda glauca vegetation in the Hetao Irrigation District, Inner Mongolia, China
Ruixiao Dong, Xinbo Wang, Yuyi Li, Hongyuan Zhang, Xiaobin Li, Jiashen Song, Fangdi Chang, Wenhao Feng, Huancheng Pang, Jing Wang
Frontiers in Microbiology.2024;[Epub] CrossRef
Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile
Maria J Ferreira, I Natalia Sierra-Garcia, Javier Cremades, Carla António, Ana M Rodrigues, Diana C G A Pinto, Helena Silva, Ângela Cunha
Journal of Applied Microbiology.2023;[Epub] CrossRef
Sustainable agricultural management of saline soils in arid and semi-arid Mediterranean regions through halophytes, microbial and soil-based technologies
Salvadora Navarro-Torre, Pedro Garcia-Caparrós, Amaia Nogales, Maria Manuela Abreu, Erika Santos, Ana Lúcia Cortinhas, Ana Delaunay Caperta
Environmental and Experimental Botany.2023; 212: 105397. CrossRef
Domestication shapes the endophytic microbiome and metabolome ofSalicornia europaea
Maria J Ferreira, I Natalia Sierra-Garcia, António Louvado, Newton C M Gomes, Sandro Figueiredo, Carla Patinha, Diana C G A Pinto, Javier Cremades, Helena Silva, Ângela Cunha
Journal of Applied Microbiology.2023;[Epub] CrossRef
Biotechnological Potential of Galophytes and Their Microbiomes for Agriculture in Russia and Kazakhstan
V. K. Chebotar, E. P. Chizhevskaya, O. V. Khonina, R. D. Kostitsin, A. A. Kurmanbayev, B. Mukhambetov, V. N. Pishchik, M. E. Baganova, N. G. Lapenko
Russian Journal of Plant Physiology.2023;[Epub] CrossRef
Alleviation of Salt Stress via Habitat-Adapted Symbiosis
Nour El Houda Rabhi, Hafsa Cherif-Silini, Allaoua Silini, Faizah N. Alenezi, Ali Chenari Bouket, Tomasz Oszako, Lassaȃd Belbahri
Forests.2022; 13(4): 586. CrossRef
Bacterial Community Structure and Potential Microbial Coexistence Mechanism Associated with Three Halophytes Adapting to the Extremely Hypersaline Environment
Lei Gao, Yin Huang, Yonghong Liu, Osama Abdalla Abdelshafy Mohamed, Xiaorong Fan, Lei Wang, Li Li, Jinbiao Ma
Microorganisms.2022; 10(6): 1124. CrossRef
A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L.
Xianchang Wang, Xu Guo, Lijuan Hou, Jiaohong Zhang, Jing Hu, Feng Zhang, Jilei Mao, Zhifen Wang, Congjing Zhang, Jinlong Han, Yanwei Zhu, Chao Liu, Jinyue Sun, Chenggang Shan
PeerJ.2022; 10: e12807. CrossRef
Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production
Madhuree Kumari, Kamal A. Qureshi, Mariusz Jaremko, James White, Sandeep Kumar Singh, Vijay Kumar Sharma, Kshitij Kumar Singh, Gustavo Santoyo, Gerardo Puopolo, Ajay Kumar
Frontiers in Plant Science.2022;[Epub] CrossRef
Profiles of Bacillus spp. Isolated from the Rhizosphere of Suaeda glauca and Their Potential to Promote Plant Growth and Suppress Fungal Phytopathogens
Ping Lu, Ke Jiang, Ya-Qiao Hao, Wan-Ying Chu, Yu-Dong Xu, Jia-Yao Yang, Jia-Le Chen, Guo-Hong Zeng, Zhou-Hang Gu, Hong-Xin Zhao
Journal of Microbiology and Biotechnology.2021; 31(9): 1231. CrossRef
The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria
Maria J. Ferreira, Angela Cunha, Sandro Figueiredo, Pedro Faustino, Carla Patinha, Helena Silva, Isabel N. Sierra-Garcia
Applied Sciences.2021; 11(5): 2233. CrossRef
Alkalinity gradients in grasslands alter soil bacterial community composition and function
Junliang Xiang, Jian Jin, Quan Liu, Yulan Huang, Wensi Wu, Ruixi Tang, Yuan Chen, Kuide Yin
Soil Science Society of America Journal.2021; 85(2): 286. CrossRef
Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh
Yaqing Pan, Peng Kang, Jinpeng Hu, Naiping Song
Science of The Total Environment.2021; 798: 149118. CrossRef
Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas
Fating Yin, Fenghua Zhang, Haoran Wang, Jian Liu
PLOS ONE.2021; 16(11): e0259515. CrossRef
Mediterranean seasonality and the halophyte Arthrocnemum macrostachyum determine the bacterial community in salt marsh soils in Southwest Spain
Miguel Camacho-Sanchez, José M. Barcia-Piedras, Susana Redondo-Gómez, Maria Camacho
Applied Soil Ecology.2020; 151: 103532. CrossRef
Dynamic changes in bacterial communities in the recirculating nutrient solution of cucumber plug seedlings cultivated in an ebb-and-flow subirrigation system
Chun-Juan Dong, Qian Li, Ling-Ling Wang, Qing-Mao Shang, Kandasamy Ulaganathan
PLOS ONE.2020; 15(4): e0232446. CrossRef
Mining the roots of various species of the halophyte Suaeda for halotolerant nitrogen-fixing endophytic bacteria with the potential for promoting plant growth
Frashad Alishahi, Hossein Ali Alikhani, Nayer Azam Khoshkholgh-Sima, Hassan Etesami
International Microbiology.2020; 23(3): 415. CrossRef
Morphophysiological Features of Some Cultivable Bacteria from Saline Soils of the Aral Sea Region
Sh. A. Begmatov, O. V. Selitskaya, L. V. Vasileva, Yu. Yu. Berestovskaja, N. A. Manucharova, N. V. Drenova
Eurasian Soil Science.2020; 53(1): 90. CrossRef
Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan
Kosuke Yamamoto, Minenosuke Matsutani, Yuh Shiwa, Taichiro Ishige, Hikaru Sakamoto, Hiromasa Saitoh, Seiya Tsushima
Microbes and Environments.2020; 35(3): n/a. CrossRef
A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars
Ting Ou, Wei-fang Xu, Fei Wang, Gary Strobel, Ze-yang Zhou, Zhong-huai Xiang, Jia Liu, Jie Xie
Computational and Structural Biotechnology Journal.2019; 17: 1091. CrossRef
Sustainability of Urban Soil Management: Analysis of Soil Physicochemical Properties and Bacterial Community Structure under Different Green Space Types
Junda Zhang, Suyan Li, Xiangyang Sun, Jing Tong, Zhen Fu, Jing Li
Sustainability.2019; 11(5): 1395. CrossRef
Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation
Bliss Ursula Furtado, Istvan Nagy, Torben Asp, Jarosław Tyburski, Monika Skorupa, Marcin Gołębiewski, Piotr Hulisz, Katarzyna Hrynkiewicz
BMC Plant Biology.2019;[Epub] CrossRef
Bacterial and Fungal Endophytic Microbiomes ofSalicornia europaea
Bliss Ursula Furtado, Marcin Gołębiewski, Monika Skorupa, Piotr Hulisz, Katarzyna Hrynkiewicz, Emma R. Master
Applied and Environmental Microbiology.2019;[Epub] CrossRef
Coastal halophytes alter properties and microbial community structure of the saline soils in the Yellow River Delta, China
Changliang Jing, Zongchang Xu, Ping Zou, Qi Tang, Yiqiang Li, Xiangwei You, Chengsheng Zhang
Applied Soil Ecology.2019; 134: 1. CrossRef
Improved germination efficiency of Salicornia ramosissima seeds inoculated with Bacillus aryabhattai SP1016‐20
Carolina Figueira, Maria J. Ferreira, Helena Silva, Angela Cunha
Annals of Applied Biology.2019; 174(3): 319. CrossRef
Salicornia europaea L. as an underutilized saline-tolerant plant inhabited by endophytic diazotrophs
Katarzyna Hrynkiewicz, Sascha Patz, Silke Ruppel
Journal of Advanced Research.2019; 19: 49. CrossRef
Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea
Kosuke Yamamoto, Yuh Shiwa, Taichiro Ishige, Hikaru Sakamoto, Keisuke Tanaka, Masataka Uchino, Naoto Tanaka, Suguru Oguri, Hiromasa Saitoh, Seiya Tsushima
Frontiers in Microbiology.2018;[Epub] CrossRef
Diversity of Bacterial Microbiota of Coastal Halophyte Limonium sinense and Amelioration of Salinity Stress Damage by Symbiotic Plant Growth-Promoting Actinobacterium Glutamicibacter halophytocola KLBMP 5180
Sheng Qin, Wei-Wei Feng, Yue-Ji Zhang, Tian-Tian Wang, You-Wei Xiong, Ke Xing, Isaac Cann
Applied and Environmental Microbiology.2018;[Epub] CrossRef
Bacterial microbiome of root-associated endophytes of Salicornia europaea in correspondence to different levels of salinity
Sonia Szymańska, Luigimaria Borruso, Lorenzo Brusetti, Piotr Hulisz, Bliss Furtado, Katarzyna Hrynkiewicz
Environmental Science and Pollution Research.2018; 25(25): 25420. CrossRef
The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing
Horatio H. Morgan, Maret du Toit, Mathabatha E. Setati
Frontiers in Microbiology.2017;[Epub] CrossRef
Effect of halotolerant endophytic bacteria isolated fromSalicornia europaeaL. on the growth of fodder beet (Beta vulgarisL.) under salt stress
Agnieszka Piernik, Katarzyna Hrynkiewicz, Anna Wojciechowska, Sonia Szymańska, Marta Izabela Lis, Adele Muscolo
Archives of Agronomy and Soil Science.2017; 63(10): 1404. CrossRef
Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica
Xue-Ying Tian, Cheng-Sheng Zhang
Frontiers in Microbiology.2017;[Epub] CrossRef

Paenibacillus insulae sp. nov., isolated from soil: Sung-Jun Cho , Sung-Heun Cho , Tae-Su Kim , Suhk-Hwan Park , Seung-Bum Kim , Geon-Hyoung Lee; J. Microbiol. 2015;53(9):588-591. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-4610-x

345 View
0 Download
5 Crossref

Abstract PDF

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80T was isolated from an island soil. The strain DS80T grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11T (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403T(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1 ω11c. Strain DS80T contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80T was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80T =JCM 17278T =KCTC 13833T).

Citations

Citations to this article as recorded by

Enhancement of stability and activity of RSD amylase from Paenibacillus lactis OPSA3 for biotechnological applications by covalent immobilization on green silver nanoparticles
Emmanuel Tobechukwu Ugwuoji, Ifeanyi S. Eze, Tochukwu Nwamaka T. Nwagu, Lewis Iheanacho Ezeogu
International Journal of Biological Macromolecules.2024; 279: 135132. CrossRef
Detergent-stable amylase production by Paenibacillus lactis strain OPSA3 isolated from soil; optimization by response surface methodology
Emmanuel Tobechukwu Ugwuoji, Tochukwu Nwamaka T. Nwagu, Lewis Iheanacho Ezeogu
Biotechnology Reports.2023; 39: e00808. CrossRef
Characterization of cellulose-degrading microbiota from the eastern subterranean termite and soil
Xianfa Xie, Alonzo B. Anderson, Latoya J. Wran, Myrna G. Serrano, Gregory A. Buck
F1000Research.2021; 6: 2082. CrossRef
Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice
Jun Zhang, Xiao-Tong Ma, Jun-Sheng Gao, Cai-Wen Zhang, Juan-Juan Zhao, Rui-Jie Zhang, Li-An Ma, Xiao-Xia Zhang
Antonie van Leeuwenhoek.2017; 110(1): 69. CrossRef
Characterization of cellulose-degrading microbiota from the eastern subterranean termite and soil
Xianfa Xie, Alonzo B. Anderson, Latoya J. Wran, Myrna G. Serrano, Gregory A. Buck
F1000Research.2017; 6: 2082. CrossRef

Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity: Jin-Kwang Kim , Myung-Suk Kang , Sung Chul Park , Kyeng-Min Kim , Kangduk Choi , Min-Ho Yoon , Wan-Taek Im; J. Microbiol. 2015;53(7):435-441. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5087-3

439 View
0 Download
36 Crossref

Abstract

The Gram-reaction-negative, strictly aerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain designated BS11T was isolated from the compost and its taxonomic position was investigated by using a polyphasic approach. Strain BS11T grew optimally at 30?7캜 and at pH 7.0 in the absence of NaCl on nutrient agar. Strain BS11T displayed ?glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to Rd. On the basis of 16S rRNA gene sequence similarity, strain BS11T was shown to belong to the family Sphingomonadaceae and was related to Sphingosinicella vermicomposti YC7378T (96.3% sequence similarity), S. xenopeptidilytica 3-2W4T (96.2%), S. microcystinivorans Y2T (96.1%), and S. soli KSL-125 T (95.9%). The G+C content of the genomic DNA was 64.9%. The major menaquinone was Q-10 and the major fatty acids were summed feature 7 (comprising C18:1 ?c/?t/?2t; 40.6%), C16:0 (22.5%), C17:1 ?c (13.7%) and C17:0 (9.1%). DNA and chemotaxonomic data supported the affiliation of strain BS11T to the genus Sphingosinicella. Strain BS11T could be differentiated genotypically and phenotypically from the recognized species of the genus Sphingosinicella. The novel isolate therefore represents a novel species, for which the name Sphingosinicella ginsenosidimutans sp. nov. is proposed, with the type strain BS11T (=KACC 16619T =JCM 18201T).

Citations

Citations to this article as recorded by

Sphingosinicella rhizophila sp. nov., Isolated from Oat (Avena sativa L.) Rhizosphere Soil
Yuze Guo, Kai Tang, Ting Yao, Jieyuzheng Zhang, Yang Liu, Jianyu Meng, Fuying Feng
Current Microbiology.2025;[Epub] CrossRef
Genomic-based taxonomic classification of the order Sphingomonadales
Yuan Wang, Hao You, Yan-Hui Kong, Cong Sun, Lin-Huan Wu, Song-Gun Kim, Jung-Sook Lee, Lin Xu, Xue-Wei Xu
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity
Muhammad Zubair Siddiqi, Ji Eun Lee, Min Ok Jun, Md. Amdadul Huq, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Evaluation of agricultural soil health after applying pyraclostrobin in wheat/maize rotation field based on the response of soil microbes
Kaixuan Hou, Chengbo Lu, Baihui Shi, Zongyuan Xiao, Xiaole Wang, Jingwen Zhang, Chao Cheng, Junchao Ma, Zhongkun Du, Bing Li, Lusheng Zhu
Agriculture, Ecosystems & Environment.2022; 340: 108186. CrossRef
Sphingosinicella terrae sp. nov. Isolated from a Desert Soil and Reclassification of Sphingomonas deserti as Sphingosinicella deserti comb. nov.
Dong Wang, Lei Dong, Neeli Habib, Feng Liu, Sohail Ahmad Jan, Jian-Yu Jiao, Min Xiao, Nimaichand Salam, Wen-Jun Li
Current Microbiology.2022;[Epub] CrossRef
Histidinibacterium aquaticum sp. nov., Isolated from Salt-Field Sea Water
Kyu-Hang Lee, Jin-Sook Park
Current Microbiology.2022;[Epub] CrossRef
Isolation, characterisation and genome analysis of a novel ginsenosides hydrolysing bacterium Ginsengibacter hankyongi gen. nov., sp. nov. isolated from soil
Muhammad Zubair Siddiqi, Md. Amdadul Huq, Wan-Taek Im
Antonie van Leeuwenhoek.2021; 114(1): 11. CrossRef
Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil
Geeta Chhetri, Minchung Kang, Jiyoun Kim, Inhyup Kim, Yoonseop So, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Luteimonas granuli sp. nov., Isolated from Granules of the Wastewater Treatment Plant
Muhammad Zubair Siddiqi, Jun Mo Yeon, Hanna Choi, Jae Hag Lee, Sang Yong Kim, Ji-Hyang Wee, Wan Taek Im
Current Microbiology.2020; 77(9): 2002. CrossRef
Hankyongella ginsenosidimutans gen. nov., sp. nov., isolated from mineral water with ginsenoside coverting activity
Muhammad Zubair Siddiqi, Wan-Taek Im
Antonie van Leeuwenhoek.2020; 113(5): 719. CrossRef
Corallincola spongiicola sp. nov., isolated from sponge
Heejae Choi, Wan-Taek Im, Jin-Sook Park
Antonie van Leeuwenhoek.2020; 113(5): 643. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef
Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil
Gyu-Min Choi, Soon-youl Lee, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 125. CrossRef
Tardibacter chloracetimidivorans gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from an agricultural soil from Jeju Island in Republic of Korea
Hyosun Lee, Dong-Uk Kim, Sooyeon Park, Jung-Hoon Yoon, Jae-Hyung Ahn, Jong-Ok Ka
Journal of Microbiology.2018; 56(5): 324. CrossRef
Aquimarina spongiicola sp. nov., isolated from spongin
Kang Duk Choi, Ga-Eun Lee, Jin-Sook Park
International Journal of Systematic and Evolutionary Microbiology.2018; 68(4): 990. CrossRef
Olivibacter ginsenosidimutans sp nov., with ginsenoside converting activity isolated from compost, and reclassification of Pseudosphingobacterium domesticum as Olivibacter domesticus comb. nov
Muhammad Zubair Siddiqi, Qingmei Liu, Soon Youl Lee, kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(8): 2509. CrossRef
Vibrio hannami sp. nov., Isolated from Seawater
Ga-Eun Lee, Wan-Taek Im, Jin-Sook Park
Current Microbiology.2018; 75(3): 278. CrossRef
Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge
Muhammad Zubair Siddiqi, Gyu-Min Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(2): 482. CrossRef
Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil
Gyu-Min Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 310. CrossRef
Flavobacterium hankyongi sp. nov., isolated from activated sludge
Qingzhen Liu, Muhammad Zubair Siddiqi, Qingmei Liu, Md. Amdadul Huq, Soon Yeol Lee, Kang-Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2018; 68(5): 1732. CrossRef
Lysobacter spongiae sp. nov., isolated from spongin
Heejae Choi, Wan-Taek Im, Jin-Sook Park
Journal of Microbiology.2018; 56(2): 97. CrossRef
Sphingomonas montis sp. nov., Isolated from Forest Soil of Low-Altitude Mountain
Dhiraj Kumar Chaudhary, Ram Hari Dahal, Jaisoo Kim
Current Microbiology.2018; 75(10): 1299. CrossRef
Brevibacterium hankyongi sp. nov., isolated from compost
Kang Duk Choi, Muhammad Zubair Siddiqi, Qingmei Liu, Siddiqi Muhammad Shafi, Yasser Durrani, Soon Yeol Lee, Myung-Suk Kang, Wan Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2783. CrossRef
Bacillus spongiae sp. nov., isolated from sponge of Jeju Island
Ga-Eun Lee, Wan-Taek Im, Jin-Sook Park
Journal of Microbiology.2018; 56(4): 217. CrossRef
Sphingomonas aquatica sp. nov., isolated from tap water
Gyu-min Choi, Jung Hun Jo, Myung-Suk Kang, Minseok S. Kim, Soon-Youl Lee, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2017; 67(4): 845. CrossRef
Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water
Muhammad Zubair Siddiqi, Gyu-Min Choi, Mi-Sun Kim, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2017; 67(8): 2665. CrossRef
Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant
Young Ki Hahn, Minseok S. Kim, Wan-Taek Im
Journal of Microbiology.2017; 55(8): 607. CrossRef
Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil
Muhammad Zubair Siddiqi, Gyu-Min Choi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2017; 67(12): 4917. CrossRef
Mucilaginibacter ginsenosidivorans sp. nov., Isolated from Soil of Ginseng Field
Minseok M. Kim, Muhammad Zubair Siddiqi, Wan-Taek Im
Current Microbiology.2017; 74(12): 1382. CrossRef
Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain
Qingmei Liu, Muhammad Zubair Siddiqi, Mi-Sun Kim, Sang Yong Kim, Wan-Taek Im
Journal of Microbiology.2017; 55(7): 525. CrossRef
Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(10): 4039. CrossRef
Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field
Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2016; 66(5): 1996. CrossRef
Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil
Muhammad Zubair Siddiqi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(9): 3449. CrossRef
Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng
Muhammad Zubair Siddiqi, Qingmei Liu, Myung-Suk Kang, Minseok S. Kim, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(3): 1125x. CrossRef
Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im, Zubair Aslam
International Journal of Systematic and Evolutionary Microbiology.2016; 66(11): 4433. CrossRef
Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(9): 3681. CrossRef

Journal Article

Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil: Juan Du , Hina Singh , Hien T.T. Ngo , KyungHwa Won , Ki-Young Kim , Tae-Hoo Yi; J. Microbiol. 2015;53(6):365-370. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-4729-9

350 View
0 Download
7 Crossref

Abstract

A novel Gram-negative, rod-shaped (0.2-0.5 um x 1.5-2.5 um), aerobic, non-motile bacterium was isolated from Gyeryongsan national park soil, Republic of Korea. The novel isolate was designated as THG-DN8.2T. The strain grows optimally at 28oC, at pH 7 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel isolate shared the highest sequence similarity with Lysobacter oryzae KCTC 22249T followed by Lysobacter yangpyeongensis KACC 11407T and Lysobacter niabensis KACC 11587T. The DNA G+C content of strain THG-DN8.2T is 66.0 mol% and ubiquinone Q-8 is the main isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The major fatty acids of strain THG-DN8.2T were identified as iso-C15:0, iso-C16:0, and C16:1w7c alcohol. The phylogenetic distinctiveness and phenotypic characteristics differentiated strain THG-DN8.2T from closely related Lysobacter species. The results of polyphasic taxonomic analysis suggest that strain THG-DN8.2T represents a novel species of the genus Lysobacter, for which the name Lysobacter tyrosinelyticus sp. nov. is proposed. The type strain is THG-DN8.2T (=KCTC 42235T =JCM 30320T).

Citations

Citations to this article as recorded by

Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
Application of Bioorganic Fertilizer on Panax notoginseng Improves Plant Growth by Altering the Rhizosphere Microbiome Structure and Metabolism
Rui Shi, Shu Wang, Bingjie Xiong, Haiyan Gu, Huiling Wang, Chao Ji, Weijia Jia, Abraham Rami Horowitz, Wenjie Zhen, Jiftah Ben Asher, Xiahong He
Microorganisms.2022; 10(2): 275. CrossRef
Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
Journal of Microbiology.2021; 59(8): 709. CrossRef
Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)
Ying Wang, Jinhua Zhang, Qiubai Zhou, Zirui Wang, Miao Gao, Xin Yang, Yu Liu, Zhengzhou Zhang, Wenhao Jiang, Chonghua Hu, Wenping Zhang
Frontiers in Microbiology.2020;[Epub] CrossRef
Lysobacter terricola sp. nov., isolated from greenhouse soil
Soo-Jin Kim, Jae-Hyung Ahn, Hang-Yeon Weon, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology.2016; 66(3): 1401. CrossRef
Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation
Xinqi Huang, Liangliang Liu, Teng Wen, Jinbo Zhang, Fenghe Wang, Zucong Cai
Applied Microbiology and Biotechnology.2016; 100(12): 5581. CrossRef
Diversity and Activity of Lysobacter Species from Disease Suppressive Soils
Ruth Gómez Expósito, Joeke Postma, Jos M. Raaijmakers, Irene De Bruijn
Frontiers in Microbiology.2015;[Epub] CrossRef

Research Support, Non-U.S. Gov'ts

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform: Yoon-Seong Jeon , Sang-Cheol Park , Jeongmin Lim , Jongsik Chun , Bong-Soo Kim; J. Microbiol. 2015;53(1):60-69. Published online January 4, 2015; DOI: https://doi.org/10.1007/s12275-015-4601-y

323 View
0 Download
34 Crossref

Abstract PDF

The cost of DNA sequencing has decreased due to advancements in Next Generation Sequencing. The number of sequences obtained from the Illumina platform is large, use of this platform can reduce costs more than the 454 pyrosequencer. However, the Illumina platform has other challenges, including bioinformatics analysis of large numbers of sequences and the need to reduce erroneous nucleotides generated at the 3􍿁-ends of the sequences. These erroneous sequences can lead to errors in analysis of microbial communities. Therefore, correction of these erroneous sequences is necessary for accurate taxonomic identification. Several studies that have used the Illumina platform to perform metagenomic analyses proposed curating pipelines to increase accuracy. In this study, we evaluated the likelihood of obtaining an erroneous microbial composition using the MiSeq 250 bp paired sequence platform and improved the pipeline to reduce erroneous identifications. We compared different sequencing conditions by varying the percentage of control phiX added, the concentration of the sequencing library, and the 16S rRNA gene target region using a mock community sample composed of known sequences. Our recommended
method
corrected erroneous nucleotides and improved identification accuracy. Overall, 99.5% of the total reads shared 95% similarity with the corresponding template sequences and 93.6% of the total reads shared over 97% similarity. This indicated that the MiSeq platform can be used to analyze microbial communities at the genus level with high accuracy. The improved analysis method recommended in this study can be applied to amplicon studies in various environments using high-throughput reads generated on the MiSeq platform.

Citations

Citations to this article as recorded by

Diversity analysis of the yeast and fungal community structure in Kazak cheese from the Yili Pastoral area in Xinjiang
Yuhui Li, Chunyan Wang, Jungang Wang
International Dairy Journal.2023; 143: 105672. CrossRef
Effects of lactic acid bacteria fermented feed and three types of lactic acid bacteria (L. plantarum, L. acidophilus, B. animalis) on intestinal microbiota and T cell polarization (Th1, Th2, Th17, Treg) in the intestinal lymph nodes and spleens of rats
Da Yoon Yu, Sang-Hyon Oh, In Sung Kim, Gwang Il Kim, Jeong A Kim, Yang Soo Moon, Jae Cheol Jang, Sang Suk Lee, Jong Hyun Jung, Hwa Chun Park, Kwang Keun Cho
Animal Bioscience.2023; 36(1): 156. CrossRef
Soil microbial community and their functional genes during grassland restoration
Jiaojiao Liao, Yanxing Dou, Xuan Yang, Shaoshan An
Journal of Environmental Management.2023; 325: 116488. CrossRef
Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation
Guoqiang Zhao, Jing Zhou, Yanning Tian, Qifeng Chen, Dongmei Mao, Jianchun Zhu, Xing Huang
Environmental Pollution.2023; 336: 122460. CrossRef
Inactivation of Antibiotic-Resistant Bacteria in Wastewater by Ozone-Based Advanced Water Treatment Processes
Takashi Azuma, Masaru Usui, Tetsuya Hayashi
Antibiotics.2022; 11(2): 210. CrossRef
LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Microbiome.2022;[Epub] CrossRef
Intestinal microbial composition changes induced by Lactobacillus plantarum GBL 16, 17 fermented feed and intestinal immune homeostasis regulation in pigs
Da Yoon Yu, Sang-Hyon Oh, In Sung Kim, Gwang Il Kim, Jeong A Kim, Yang Soo Moon, Jae Cheol Jang, Sang Suk Lee, Jong Hyun Jung, Jun Park, Kwang Keun Cho
Journal of Animal Science and Technology.2022; 64(6): 1184. CrossRef
Investigating the core microbiota and its influencing factors in traditional Chinese pickles
Feiyu An, Huijun Sun, Junrui Wu, Chunyan Zhao, Tong Li, Heting Huang, Qiang Fang, Endong Mu, Rina Wu
Food Research International.2021; 147: 110543. CrossRef
Soil remediation approach and bacterial community structure in a long-term contaminated soil by a mining spill (Aznalcóllar, Spain)
M. Paniagua-López, M. Vela-Cano, D. Correa-Galeote, F. Martín-Peinado, F.J. Martínez Garzón, C. Pozo, J. González-López, M. Sierra Aragón
Science of The Total Environment.2021; 777: 145128. CrossRef
Effects of natural sunlight on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in wastewater and river water
Takashi Azuma, Tetsuya Hayashi
Science of The Total Environment.2021; 766: 142568. CrossRef
On-site chlorination responsible for effective disinfection of wastewater from hospital
Takashi Azuma, Tetsuya Hayashi
Science of The Total Environment.2021; 776: 145951. CrossRef
Disinfection of Antibiotic-resistant Bacteria in Sewage and Hospital Effluent by Ozonation
Takashi Azuma, Tetsuya Hayashi
Ozone: Science & Engineering.2021; 43(5): 413. CrossRef
Analysis of bacterial diversity and biogenic amines content during fermentation of farmhouse sauce from Northeast China
Yu Hao, Bo Sun
Food Control.2020; 108: 106861. CrossRef
Performance of enhanced anaerobic digestion with different pyrolysis biochars and microbial communities
Ruixia Shen, Yong Jing, Jing Feng, Juan Luo, Jiadong Yu, Lixin Zhao
Bioresource Technology.2020; 296: 122354. CrossRef
Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier
Valerie Cortez, David F. Boyd, Jeremy Chase Crawford, Bridgett Sharp, Brandi Livingston, Hannah M. Rowe, Amy Davis, Ramzi Alsallaq, Camenzind G. Robinson, Peter Vogel, Jason W. Rosch, Elisa Margolis, Paul G. Thomas, Stacey Schultz-Cherry
Nature Communications.2020;[Epub] CrossRef
Metagenomic analysis of bacterial community structure and functions during the fermentation of da-jiang, a Chinese traditional fermented food
Mengxi Xie, Feiyu An, Yue Zhao, Rina Wu, Junrui Wu
LWT.2020; 129: 109450. CrossRef
Relationship between nasopharyngeal microbiota and patient’s susceptibility to viral infection
Grégory Dubourg, Sophie Edouard, Didier Raoult
Expert Review of Anti-infective Therapy.2019; 17(6): 437. CrossRef
Structure and Diversity of Soil Bacterial Communities in Offshore Islands
Yu-Te Lin, Yu-Fei Lin, Isheng J. Tsai, Ed-Haun Chang, Shih-Hao Jien, Yen-Ju Lin, Chih-Yu Chiu
Scientific Reports.2019;[Epub] CrossRef
Meta‐omics reveal microbial assortments and key enzymes in bean sauce mash, a traditional fermented soybean product
Mengxi Xie, Feiyu An, Junrui Wu, Yiming Liu, Haishu Shi, Rina Wu
Journal of the Science of Food and Agriculture.2019; 99(14): 6522. CrossRef
Insights into evolutionary trends in molecular biology tools in microbial screening for biohydrogen production through dark fermentation
Gopalakrishnan Kumar, Si-Kyung Cho, Periyasamy Sivagurunathan, Parthiban Anburajan, Durga Madhab Mahapatra, Jeong-Hoon Park, Arivalagan Pugazhendhi
International Journal of Hydrogen Energy.2018; 43(43): 19885. CrossRef
Analyses of microbial community of naturally homemade soybean pastes in Liaoning Province of China by Illumina Miseq Sequencing
Xiaodong Sun, Guozhong Lyu, Yushi Luan, Zhihui Zhao, Hong Yang, Dan Su
Food Research International.2018; 111: 50. CrossRef
Effects of Rubus coreanus byproducts on intestinal microbiota and the immune modulation
Da Yoon Yu, Sung Hak Kim, Jeong A Kim, In Sung Kim, Yang Soo Moon, Sang Suk Lee, Hwa Chun Park, Jong Hyun Jung, Yi Hyung Chung, Dae Keun Shin, Ki Chang Nam, In Soon Choi, Kwang Keun Cho
Asian-Australasian Journal of Animal Sciences.2018; 31(3): 429. CrossRef
Sequencing Batch Reactor and Bacterial Community in Aerobic Granular Sludge for Wastewater Treatment of Noodle-Manufacturing Sector
Tang Chinh, Phung Hieu, Bui Cuong, Nguyen Linh, Nguyen Lan, Nguyen Nguyen, Nguyen Hung, Le Hien
Applied Sciences.2018; 8(4): 509. CrossRef
An improved metagenomic strategy reveals an unprecedentedly high level of intragenomic polymorphism of ribosomal DNA in three species of Camellia
Yang Shao, Min Zhang, Ying Xu, Yong‐Qing Zhu, Takahiro Yonezawa, Yu‐Guo Wang, Zhi‐Ping Song, Wen‐Ju Zhang
Journal of Systematics and Evolution.2018; 56(3): 250. CrossRef
Comparison of intestinal microbiota and activities of digestive and immune-related enzymes of sea cucumber Apostichopus japonicus in two habitats
Qi Wang, Xiumei Zhang, Muyan Chen, Wentao Li, Peidong Zhang
Journal of Oceanology and Limnology.2018; 36(3): 990. CrossRef
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Kelly D. Goodwin, Luke R. Thompson, Bernardo Duarte, Tim Kahlke, Andrew R. Thompson, João C. Marques, Isabel Caçador
Frontiers in Marine Science.2017;[Epub] CrossRef
Differences in root-associated bacterial communities among fine root branching orders of poplar (Populus × euramericana (Dode) Guinier.)
Qitong Wang, Nian Wang, Yanping Wang, Qingkui Wang, Baoli Duan
Plant and Soil.2017; 421(1-2): 123. CrossRef
Advanced nitrogen removal from the biological secondary effluent of dyeing wastewater via a biological–ferric–carbon nitrification and denitrification process
Hong Chen, Gang Xue, Mengran Jiang, Yuying Cheng
RSC Advances.2016; 6(108): 106951. CrossRef
Microbial electrolysis cell to treat hydrothermal liquefied wastewater from cornstalk and recover hydrogen: Degradation of organic compounds and characterization of microbial community
Ruixia Shen, Zhidan Liu, Yanhong He, Yuanhui Zhang, Jianwen Lu, Zhangbing Zhu, Buchun Si, Chong Zhang, Xin-Hui Xing
International Journal of Hydrogen Energy.2016; 41(7): 4132. CrossRef
DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses
Marie Lisandra Zepeda-Mendoza, Kristine Bohmann, Aldo Carmona Baez, M. Thomas P. Gilbert
BMC Research Notes.2016;[Epub] CrossRef
Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken)
Fabiola Valenzuela-González, Marcel Martínez-Porchas, Enrique Villalpando-Canchola, Francisco Vargas-Albores
Journal of Microbiological Methods.2016; 122: 38. CrossRef
Adaptive evolution and metabolic engineering of a cellobiose- and xylose- negative Corynebacterium glutamicum that co-utilizes cellobiose and xylose
Jungseok Lee, Jack N. Saddler, Youngsoon Um, Han Min Woo
Microbial Cell Factories.2016;[Epub] CrossRef
Bacteria Associated WithPiezodorus guildinii(Hemiptera: Pentatomidae), With Special Reference to Those Transmitted by Feeding
Claudia Husseneder, Jong-Seok Park, Andrea Howells, Chinmay V. Tikhe, Jeffrey A. Davis
Environmental Entomology.2016; : nvw112. CrossRef
Fecal Microbiota Analysis: An Overview of Sample Collection Methods and Sequencing Strategies
Vincent Thomas, James Clark, Joël Doré
Future Microbiology.2015; 10(9): 1485. CrossRef

Distinct Patterns of Marine Bacterial Communities in the South and North Pacific Oceans: Sung-Suk Suh , Mirye Park , Jinik Hwang , Sukchan Lee , Youngjae Chung , Taek-Kyun Lee; J. Microbiol. 2014;52(10):834-841. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4287-6

293 View
0 Download
12 Crossref

Abstract PDF

The study of oceanic microbial communities is crucial for our understanding of the role of microbes in terms of biomass, diversity and ecosystem function. In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively. Summer and winter sampling from each water mass revealed highly diverse bacterial communities, containing ~900 Operational Taxonomic Units (OTUs). The microbial distribution and highly heterogeneous composition observed at both sampling sites were different from those of most macroorganisms. The bacterial communities in the seawater at both sites were most abundant in Proteobacteria during the summer in Gosung and in Bacterioidetes during the winter. The proportion of Cyanobacteria was higher in summer than in winter in Chuuk and similar in Gosung. Additionally, the microbial community during summer in Gosung was significantly different from other communities observed based on the unweighted UniFrac distance. These data suggest that in both oceanic areas sampled, the bacterial communities had distinct distribution patterns with spatially- and temporally-heterogeneous distributions.

Citations

Citations to this article as recorded by

Metavirome Profiling and Dynamics of the DNA Viral Community in Seawater in Chuuk State, Federated States of Micronesia
Seung Won Jung, Kang Eun Kim, Hyun-Jung Kim, Taek-Kyun Lee
Viruses.2023; 15(6): 1293. CrossRef
The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean
Zhichen Jiang, Sizhen Liu, Dechao Zhang, Zhongli Sha
Microbial Ecology.2023; 86(4): 2781. CrossRef
Exploring the plankton bacteria diversity and distribution patterns in the surface water of northwest pacific ocean by metagenomic methods
Yafei Wang, Hongmei Lin, Ranran Huang, Weidong Zhai
Frontiers in Marine Science.2023;[Epub] CrossRef
Characterization of bacterial community structure in two alcyonacean soft corals (Litophyton sp. and Sinularia sp.) from Chuuk, Micronesia
Joon Sang Park, Jeonghoon Han, Sung-Suk Suh, Hyun-Jung Kim, Taek-Kyun Lee, Seung Won Jung
Coral Reefs.2022; 41(3): 563. CrossRef
Influences of Seasonal Monsoons on the Taxonomic Composition and Diversity of Bacterial Community in the Eastern Tropical Indian Ocean
Ping Gao, Guangxun Du, Duo Zhao, Qinsheng Wei, Xuelei Zhang, Lingyun Qu, Xianzhe Gong
Frontiers in Microbiology.2021;[Epub] CrossRef
Bacterial and Fungal Diversity in Sediment and Water Column From the Abyssal Regions of the Indian Ocean
Natasha Maria Barnes, Samir R. Damare, Belle Damodara Shenoy
Frontiers in Marine Science.2021;[Epub] CrossRef
Diversity and biogeography of picoplankton communities from the Straits of Malacca to the South China Sea
Zhao-Yu Jiang, Fu-Lin Sun
Oceanological and Hydrobiological Studies.2020; 49(1): 23. CrossRef
Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences
Rongjun Shi, Jiajun Li, Zhanhui Qi, Zhe Zhang, Huaxue Liu, Honghui Huang
Biologia.2018; 73(2): 197. CrossRef
Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean
Yuan-Yuan Li, Xiao-Huang Chen, Zhang-Xian Xie, Dong-Xu Li, Peng-Fei Wu, Ling-Fen Kong, Lin Lin, Shuh-Ji Kao, Da-Zhi Wang
Frontiers in Microbiology.2018;[Epub] CrossRef
Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea
Jin Zhou, Xiao Song, Chun-Yun Zhang, Guo-Fu Chen, Yong-Min Lao, Hui Jin, Zhong-Hua Cai
Microbial Ecology.2018; 76(3): 592. CrossRef
A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean
Jing Wang, Jinjun Kan, Laura Borecki, Xiaodong Zhang, Dongxiao Wang, Jun Sun
Acta Oceanologica Sinica.2016; 35(6): 85. CrossRef
Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea
Sung-Suk Suh, Mirye Park, Jinik Hwang, Eui-Joon Kil, Seung Won Jung, Sukchan Lee, Taek-Kyun Lee, Torsten Thomas
PLOS ONE.2015; 10(6): e0131633. CrossRef

Note] Oceanobacillus gochujangensis sp. nov., Isolated from gochujang a Traditional Korean Fermented Food: Seo-Jung Jang , Yu-Jin Kim , Sul-Hee Lee , Young-Seo Park , Jung-Min Park , Dong-Hoon Bai; J. Microbiol. 2014;52(12):1050-1055. Published online July 30, 2014; DOI: https://doi.org/10.1007/s12275-014-4220-z

342 View
0 Download
4 Crossref

Abstract PDF

A Gram-stain-positive, polar flagella-containing, rod-shaped, obligate aerobic, endospore-forming bacterium, strain TK1655T, was isolated from the traditional Korean food gochujang. The 16S rRNA sequence of strain TK1655T was a member of the genus Oceanobacillus similar to that of the type strain of Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557T (97.2%), O. oncorhynchi subsp. oncorhynchi JCM 12661T (97.1%), O. locisalsi KCTC 13253T (97.0%), and O. sojae JCM 15792T (96.9%). Strain TK1655T was oxidase and catalase positive. Colonies were circular, smooth, low convex, cream in colour, and measured about 0.5–1.0 mm in diameter. The range for growth was 20–40°C (optimal, 30°C), pH 6.0– 10.0 (optimal, 7.0), and 2–16% (w/v) NaCl (optimal, 2%). Additionally, the cells contained meso-DAP, and the predominant isoprenoid quinone was MK-7. The complex polar lipids were consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC). The major cellular fatty acid components were iso-C15:0, anteiso-C15:0, iso-C16:0, and anteiso-C17:0, and the DNA G+C content was 40.5%. DNA-DNA relatedness of our novel strain and reference strain O. locisalsi KCTC 13253T, O. oncorhynchi subsp. incaldanensis DSM 16557T, O. oncorhynchi subsp. oncorhynchi JCM 12661T was 45.7, 43.8, and 41.9%. From the
results
of phenotypic, chemotaxonomic, and phylogenetic analyses of strain TK1655T, we propose the novel species Oceanobacillus gochujangensis sp. nov. The type strain is TK1655T (=KCCM 101304T =KCTC 33014T =CIP 110582T =NBRC 109637T).

Citations

Citations to this article as recorded by

Microbiota dynamics and volatile compounds in lupine based Moromi fermented at different salt concentrations
Rebekka H. Lülf, Rudi F. Vogel, Matthias A. Ehrmann
International Journal of Food Microbiology.2021; 354: 109316. CrossRef
Cell envelop is the key site for Cr(Ⅵ) reduction by Oceanobacillus oncorhynchi W4, a newly isolated Cr(Ⅵ) reducing bacterium
Qiang Zeng, Yuting Hu, Yiran Yang, Liang Hu, Hui Zhong, Zhiguo He
Journal of Hazardous Materials.2019; 368: 149. CrossRef
Microbial communities and their predicted metabolic functions in a desiccating acid salt lake
Elena Zaikova, Kathleen C. Benison, Melanie R. Mormile, Sarah Stewart Johnson
Extremophiles.2018; 22(3): 367. CrossRef
Oceanobacillus bengalensis sp. nov., a bacterium isolated from seawater of the Bay of Bengal
Ouyang Yongchang, Wenzhou Xiang, Guanghua Wang
Antonie van Leeuwenhoek.2015; 108(5): 1189. CrossRef

Pyrosequencing-based Analysis of Fecal Microbial Communities in Three Purebred Pig Lines: Edward Alain B. Pajarillo , Jong Pyo Chae , Marilen P. Balolong , Hyeun Bum Kim , Kang-Seok Seo , Dae-Kyung Kang; J. Microbiol. 2014;52(8):646-651. Published online July 18, 2014; DOI: https://doi.org/10.1007/s12275-014-4270-2

454 View
0 Download
82 Crossref

Abstract PDF

This study examined the fecal bacterial diversity of 15-week-old pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Citations

Citations to this article as recorded by

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency
Naomi Sarpong, Jana Seifert, Jörn Bennewitz, Markus Rodehutscord, Amélia Camarinha-Silva
Frontiers in Microbiology.2024;[Epub] CrossRef
Characteristics of gut microbiota and metabolomic of Hainan Tunchang pigs at various growth stages
Zhen Tan, Jie Li, Yingzhi He, Feifan Wang, Qian Xiao
Gene.2024; 900: 148161. CrossRef
Effects of dietary xylanase supplementation on growth performance, intestinal health, and immune response of nursery pigs fed diets with reduced metabolizable energy
Jonathan T Baker, Marcos Elias Duarte, Sung Woo Kim
Journal of Animal Science.2024;[Epub] CrossRef
Dietary supplementation with Lactiplantibacillus plantarum P-8 improves the growth performance and gut microbiota of weaned piglets
Jie Yu, Bin Zuo, Qi Li, Feiyan Zhao, Junjun Wang, Weiqiang Huang, Zhihong Sun, Yongfu Chen, Stephan Schmitz-Esser
Microbiology Spectrum.2024;[Epub] CrossRef
A Comparative Study on the Growth Performance and Gut Microbial Composition of Duroc and Yorkshire Boars
Junhua Du, Mailin Gan, Zhongwei Xie, Gao Du, Yi Luo, Bin Liu, Kangping Zhu, Lei Chen, Ye Zhao, Lili Niu, Yan Wang, Jingyong Wang, Li Zhu, Linyuan Shen
Genes.2023; 14(9): 1726. CrossRef
The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets
Ling Li, Shuai Li, Junyi Luo, Ting Chen, Qianyun Xi, Yongliang Zhang, Jiajie Sun
BMC Veterinary Research.2023;[Epub] CrossRef
Intestinal microbiota disturbance affects the occurrence of African swine fever
Cheng-Xing Long, Jie-Qi Wu, Zhou-Jin Tan
Animal Biotechnology.2023; 34(4): 1040. CrossRef
Role of genetic factors in different swine breeds exhibiting varying levels of resistance/susceptibility to PRRSV
Xiangbin You, Gan Li, Ying Lei, Zhiqian Xu, Ping Zhang, Youbing Yang
Virus Research.2023; 326: 199057. CrossRef
Effect of providing citrus pulp-integrated diet on fecal microbiota and serum and fecal metabolome shifts in crossbred pigs
Dhekra Belloumi, Salvador Calvet, Marta Isabel Roca, Pablo Ferrer, Ana Jiménez-Belenguer, María Cambra-López, Paloma García-Rebollar, Eric Climent, Juan Martínez-Blanch, Marta Tortajada, Empar Chenoll, Almudena Bermejo, Alba Cerisuelo
Scientific Reports.2023;[Epub] CrossRef
Impact of Early Weaning on Development of the Swine Gut Microbiome
Benoit St-Pierre, Jorge Yair Perez Palencia, Ryan S. Samuel
Microorganisms.2023; 11(7): 1753. CrossRef
Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs
Taoran Du, Pinghua Li, Qing Niu, Guang Pu, Binbin Wang, Gensheng Liu, Pinghui Li, Peipei Niu, Zongping Zhang, Chengwu Wu, Liming Hou, Mette Skou Hedemann, Qingbo Zhao, Ruihua Huang
Microorganisms.2023; 11(10): 2474. CrossRef
The Role of Gut Microbiota in the Skeletal Muscle Development and Fat Deposition in Pigs
Qi Han, Xingguo Huang, Fuyong Yan, Jie Yin, Yingping Xiao
Antibiotics.2022; 11(6): 793. CrossRef
Intestinal Exposure to Ceftiofur and Cefquinome after Intramuscular Treatment and the Impact of Ceftiofur on the Pig Fecal Microbiome and Resistome
Sofie Rutjens, Nick Vereecke, Ward De Spiegelaere, Siska Croubels, Mathias Devreese
Antibiotics.2022; 11(3): 342. CrossRef
Dynamic Distribution of Gut Microbiota in Pigs at Different Growth Stages: Composition and Contribution
Yuheng Luo, Wen Ren, Hauke Smidt, André-Denis G. Wright, Bing Yu, Ghislain Schyns, Ursula M. McCormack, Aaron J. Cowieson, Jie Yu, Jun He, Hui Yan, Jinlong Wu, Roderick I. Mackie, Daiwen Chen, Cheng-Yuan Kao, Rustem Ilyasov
Microbiology Spectrum.2022;[Epub] CrossRef
Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages
Jianfeng Ma, Jingyun Chen, Mailin Gan, Lei Chen, Ye Zhao, Yan Zhu, Lili Niu, Shunhua Zhang, Li Zhu, Linyuan Shen
Animals.2022; 12(13): 1607. CrossRef
Effects of Bacillus amyloliquefaciens TL106 Isolated from Tibetan Pigs on Probiotic Potential and Intestinal Microbes in Weaned Piglets
Haitao Du, Wangyuan Yao, Muhammad Fakhar-e-Alam Kulyar, Yanmei Ding, Huaisen Zhu, Huachun Pan, Kewei Li, Zeeshan Ahmad Bhutta, Suozhu Liu, Jiakui Li, Hui Wang
Microbiology Spectrum.2022;[Epub] CrossRef
Effect of sex on the gut microbiota characteristics of passerine migratory birds
Rongfei Yan, Meixia Lu, Lishi Zhang, Jiyuan Yao, Shi Li, Yunlei Jiang
Frontiers in Microbiology.2022;[Epub] CrossRef
Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine
Yuqing He, Francesco Tiezzi, Jicai Jiang, Jeremy Howard, Yijian Huang, Kent Gray, Jung-Woo Choi, Christian Maltecca
Journal of Animal Science.2022;[Epub] CrossRef
Remodeling of the microbiota improves the environmental adaptability and disease resistance in Tibetan pigs
Zhenyu Chang, Suxue Bo, Qingqing Xiao, Yu Wang, Xi Wu, Yuxuan He, Mujahid Iqbal, Yourong Ye, Peng Shang
Frontiers in Microbiology.2022;[Epub] CrossRef
Batch and sampling time exert a larger influence on the fungal community than gastrointestinal location in model animals: A meaningful case study
Jiayan Li, Daiwen Chen, Bing Yu, Jun He, Zhiqing Huang, Ping Zheng, Xiangbing Mao, Hua Li, Jie Yu, Junqiu Luo, Hui Yan, Yuheng Luo
Frontiers in Nutrition.2022;[Epub] CrossRef
Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig
Cheng-xing Long, Jie-qi Wu, Zhou-jin Tan, Sheng-ping Wang, Takashi Yazawa
BioMed Research International.2022; 2022: 1. CrossRef
Alterations in gut microbiota improve SCFA production and fiber utilization in Tibetan pigs fed alfalfa diet
Qingtao Gao, Guangming Sun, Jiujun Duan, Chengzeng Luo, Cidan Yangji, Ruqing Zhong, Liang Chen, Yanbin Zhu, Basang Wangdui, Hongfu Zhang
Frontiers in Microbiology.2022;[Epub] CrossRef
Comparative Study on Jejunal Immunity and Microbial Composition of Growing-Period Tibetan Pigs and Duroc × (Landrace × Yorkshire) Pigs
Yuting Yang, Yongxiang Li, Yanggang Xie, Shiyan Qiao, Lijie Yang, Hongbin Pan
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Identification of Gut Microbiota Affecting Fiber Digestibility in Pigs
Qing Niu, Guang Pu, Lijuan Fan, Chen Gao, Tingxu Lan, Chenxi Liu, Taoran Du, Sung Woo Kim, Peipei Niu, Zongping Zhang, Pinghua Li, Ruihua Huang
Current Issues in Molecular Biology.2022; 44(10): 4557. CrossRef
The Impact of Genetics on Gut Microbiota of Growing and Fattening Pigs under Moderate N Restriction
Laura Sarri, Sandra Costa-Roura, Joaquim Balcells, Ahmad Reza Seradj, Gabriel de la Fuente
Animals.2021; 11(10): 2846. CrossRef
Identification of the gut microbiota biomarkers associated with heat cycle and failure to enter oestrus in gilts
Zhong Wang, Hao Fu, Yunyan Zhou, Min Yan, Dong Chen, Ming Yang, Shijun Xiao, Congying Chen, Lusheng Huang
Microbial Biotechnology.2021; 14(4): 1316. CrossRef
Evolution of the Gut Microbiota and Its Fermentation Characteristics of Ningxiang Pigs at the Young Stage
Hao Li, Longteng Ma, Zhiqing Li, Jie Yin, Bie Tan, Jiashun Chen, Qian Jiang, Xiaokang Ma
Animals.2021; 11(3): 638. CrossRef
The Nutritional Significance of Intestinal Fungi: Alteration of Dietary Carbohydrate Composition Triggers Colonic Fungal Community Shifts in a Pig Model
Yuheng Luo, Jiayan Li, Hua Zhou, Bing Yu, Jun He, Aimin Wu, Zhiqing Huang, Ping Zheng, Xiangbing Mao, Jie Yu, Hua Li, Huifen Wang, Quyuan Wang, Hui Yan, Daiwen Chen, Danilo Ercolini
Applied and Environmental Microbiology.2021;[Epub] CrossRef
Fecal microbial composition and functional diversity of Wuzhishan pigs at different growth stages
Mingying Shao, Zhixin Wang, Yingzhi He, Zhen Tan, Jibin Zhang
AMB Express.2021;[Epub] CrossRef
Comparison of cecal microbiota composition in hybrid pigs from two separate three-way crosses
Yuting Yang, Liyan Shen, Huan Gao, Jinming Ran, Xian Li, Hengxin Jiang, Xueyan Li, Zhenhui Cao, Ying Huang, Sumei Zhao, Chunlian Song, Hongbin Pan
Animal Bioscience.2021; 34(7): 1202. CrossRef
Effects of the Inclusion of Fermented Mulberry Leaves and Branches in the Gestational Diet on the Performance and Gut Microbiota of Sows and Their Offspring
Yuping Zhang, Chang Yin, Martine Schroyen, Nadia Everaert, Teng Ma, Hongfu Zhang
Microorganisms.2021; 9(3): 604. CrossRef
Timely Control of Gastrointestinal Eubiosis: A Strategic Pillar of Pig Health
Paolo Trevisi, Diana Luise, Federico Correa, Paolo Bosi
Microorganisms.2021; 9(2): 313. CrossRef
Comparative analysis of the rectal and caecal microbial community composition and function in adult Erhualian and Sushan pigs
B. Li, S. Ren, W. Zhao, X. Wang, F. Tu
Journal of Animal and Feed Sciences.2021; 30(3): 248. CrossRef
Whole-metagenome shotgun sequencing of pig faecal microbiome
Letterio Giuffrè, Domenico Giosa, Grazia Galeano, Riccardo Aiese Cigliano, Andreu Paytuví-Gallart, Anna Maria Sutera, Giuseppe Tardiolo, Alessandro Zumbo, Orazio Romeo, Enrico D’Alessandro
Italian Journal of Animal Science.2021; 20(1): 1147. CrossRef
Comparison of early-life jejunal microbiota diversity in two pig breeds
Yuting Yang, Huan Gao, Jinming Ran, Ying Huang, Minghua Yang, Lijie Yang, Sumei Zhao, Shiyan Qiao, Hongbin Pan
Czech Journal of Animal Science.2021; 66(11): 459. CrossRef
Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
Ann M. Arfken, Juli Foster Frey, Katie Lynn Summers
Microorganisms.2020; 8(6): 868. CrossRef
Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract
Shi Tang, Ying Xin, Yunlong Ma, Xuewen Xu, Shuhong Zhao, Jianhua Cao
Frontiers in Microbiology.2020;[Epub] CrossRef
Interactions between host and gut microbiota in domestic pigs: a review
Yadnyavalkya Patil, Ravi Gooneratne, Xiang-Hong Ju
Gut Microbes.2020; 11(3): 310. CrossRef
Dietary Supplementation with Compound Probiotics and Berberine Alters Piglet Production Performance and Fecal Microbiota
Xiaoxiang Xu, Canyu Yang, Juan Chang, Ping Wang, Qingqiang Yin, Chaoqi Liu, Tianzeng Gao, Xiaowei Dang, Fushan Lu
Animals.2020; 10(3): 511. CrossRef
The fungal community and its interaction with the concentration of short‐chain fatty acids in the faeces of Chenghua, Yorkshire and Tibetan pigs
Jiayan Li, Daiwen Chen, Bing Yu, Jun He, Zhiqing Huang, Xiangbing Mao, Ping Zheng, Jie Yu, Junqiu Luo, Gang Tian, Yuheng Luo
Microbial Biotechnology.2020; 13(2): 509. CrossRef
Composition and functional diversity of fecal bacterial community of wild boar, commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing
Jinqing Huang, Wenjuan Zhang, Rong Fan, Zhanggen Liu, Tao Huang, Junyi Li, Tonghao Du, Tao Xiong
Archives of Microbiology.2020; 202(4): 843. CrossRef
Gut microbiome composition differences among breeds impact feed efficiency in swine
Matteo Bergamaschi, Francesco Tiezzi, Jeremy Howard, Yi Jian Huang, Kent A. Gray, Constantino Schillebeeckx, Nathan P. McNulty, Christian Maltecca
Microbiome.2020;[Epub] CrossRef
A glance at the gut microbiota of five experimental animal species through fecal samples
Zhiguang Xiang, Hua Zhu, Bochao Yang, Hang Fan, Jianguo Guo, Jiangning Liu, Qi Kong, Qingfeng Teng, Haiquan Shang, Lei Su, Chuan Qin
Scientific Reports.2020;[Epub] CrossRef
Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania
Robab Katani, Megan A. Schilling, Beatus Lyimo, Triza Tonui, Isabella M. Cattadori, Ernest Eblate, Andimile Martin, Anna B. Estes, Teresia Buza, Dennis Rentsch, Karen W. Davenport, Blake T. Hovde, Samson Lyimo, Lydia Munuo, Francesca Stomeo, Christian Tia
Scientific Reports.2019;[Epub] CrossRef
The effect of fumonisins producing Fusarium verticillioides on the microbiota in pig caecum
Huu Anh Dang, Attila Zsolnai, Melinda Kovács, Brigitta Bóta, Gábor Mihucz, Roland Pósa, Kinga Marosi, Mariam Kachlek, Judit Szabó-Fodor
Acta Veterinaria Brno.2019; 88(1): 65. CrossRef
Fecal Microbiota and Its Correlation With Fatty Acids and Free Amino Acids Metabolism in Piglets After a Lactobacillus Strain Oral Administration
Dongyan Zhang, Hui Liu, Sixin Wang, Wei Zhang, Jing Wang, Hongwu Tian, Yamin Wang, Haifeng Ji
Frontiers in Microbiology.2019;[Epub] CrossRef
Comparative metabolomic analysis of caecal digesta between Jinhua pig and Landrace pig
Yujie Gong, Xiaoting Zou, Wenrui Xia, Xueting Wen, Xiaojun Zhang, Yingping Xiao, Hua Yang
Czech Journal of Animal Science.2019; 64(8): 332. CrossRef
Piglet gut microbial shifts early in life: causes and effects
Robin B. Guevarra, Jun Hyung Lee, Sun Hee Lee, Min-Jae Seok, Doo Wan Kim, Bit Na Kang, Timothy J. Johnson, Richard E. Isaacson, Hyeun Bum Kim
Journal of Animal Science and Biotechnology.2019;[Epub] CrossRef
Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age‐related dietary changes
Qiaoli Yang, Xiaoyu Huang, Pengfei Wang, Zunqiang Yan, Wenyang Sun, Shengguo Zhao, Shuangbao Gun
MicrobiologyOpen.2019;[Epub] CrossRef
Oral Metallo-Beta-Lactamase Protects the Gut Microbiome From Carbapenem-Mediated Damage and Reduces Propagation of Antibiotic Resistance in Pigs
Sheila Connelly, Brian Fanelli, Nur A. Hasan, Rita R. Colwell, Michael Kaleko
Frontiers in Microbiology.2019;[Epub] CrossRef
Different gut microbiome composition in obese Guizhou minipigs between female and castrated male
Gang Yao, Shuguang Wu, Xianchun Zeng, Hai Zhao, Guoqi Wang, Mingfei Chen, Ning Qian
Folia Microbiologica.2019; 64(6): 889. CrossRef
Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass
Anne Mette Jakobsen, Martin Iain Bahl, Tasja Buschhardt, Tina Beck Hansen, Waleed Abu Al-Soud, Asker D. Brejnrod, Søren J. Sørensen, Truls Nesbakken, Søren Aabo
International Journal of Food Microbiology.2019; 295: 8. CrossRef
Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age
Hua Yang, Yingping Xiao, Junjun Wang, Yun Xiang, Yujie Gong, Xueting Wen, Defa Li
Journal of Microbiology.2018; 56(5): 346. CrossRef
A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research
Sylvia Brugman, Wakako Ikeda-Ohtsubo, Saskia Braber, Gert Folkerts, Corné M. J. Pieterse, Peter A. H. M. Bakker
Frontiers in Nutrition.2018;[Epub] CrossRef
Gut Microbiota Is a Major Contributor to Adiposity in Pigs
Hua Yang, Yun Xiang, Kelsy Robinson, Junjun Wang, Guolong Zhang, Jiangchao Zhao, Yingping Xiao
Frontiers in Microbiology.2018;[Epub] CrossRef
Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions
Afnan Khalil Ahmad Suleiman, Késia Silva Lourenço, Leonardo Machado Pitombo, Lucas William Mendes, Luiz Fernando Wurdig Roesch, Agata Pijl, Janaína Braga Carmo, Heitor Cantarella, Eiko Eurya Kuramae
Science of The Total Environment.2018; 631-632: 1089. CrossRef
The Effect of Feeding Cocoa Powder and Lactobacillus rhamnosus on the Composition and Function of Pig Intestinal Microbiome
Gloria I Solano-Aguilar, Sukla Lakshman, Saebyeol Jang, Ethiopia Beshah, Yue Xie, Masoumeh Sikaroodi, Richi Gupta, Bryan Vinyard, Aleksey Molokin, Joseph F Urban, Patrick Gillevet, Cindy D Davis
Current Developments in Nutrition.2018; 2(5): nzy011. CrossRef
Exploratory Analysis of the Microbiological Potential for Efficient Utilization of Fiber Between Lantang and Duroc Pigs
Penghui Cheng, Yan Wang, Juanboo Liang, Yinbao Wu, Andredenis Wright, Xindi Liao
Frontiers in Microbiology.2018;[Epub] CrossRef
The significance of the diversity and composition of the cecal microbiota of the Tibetan swine
Weiping Yang, Haiyun Xin, Fangjun Cao, Jinxing Hou, Li Ma, Lijuan Bao, Fangyuan Wang, Zhantao Yu, Binyun Cao
Annals of Microbiology.2018; 68(4): 185. CrossRef
Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs
Amelia Camarinha-Silva, Maria Maushammer, Robin Wellmann, Marius Vital, Siegfried Preuss, Jörn Bennewitz
Genetics.2017; 206(3): 1637. CrossRef
Probiotic roles ofLactobacillussp. in swine: insights from gut microbiota
V.D.V. Valeriano, M.P. Balolong, D.-K. Kang
Journal of Applied Microbiology.2017; 122(3): 554. CrossRef
In vitro Interaction between Fumonisin B1 and the Intestinal Microflora of Pigs
HUU ANH DANG, ATTILA ZSOLNAI, MELINDA KOVACS, ISTVÁN BORS, ANDRÁS BÓNAI, BRIGITTA BÓTA, JUDIT SZABÓ-FODOR
Polish Journal of Microbiology.2017; 66(2): 245. CrossRef
Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets
Shijuan Yan, Cui Zhu, Ting Yu, Wenjie Huang, Jianfeng Huang, Qian Kong, Jingfang Shi, Zhongjian Chen, Qinjian Liu, Shaolei Wang, Zongyong Jiang, Zhuang Chen
Frontiers in Microbiology.2017;[Epub] CrossRef
Meta-analysis To Define a Core Microbiota in the Swine Gut
Devin B. Holman, Brian W. Brunelle, Julian Trachsel, Heather K. Allen, Holly Bik
mSystems.2017;[Epub] CrossRef
The fecal microbiota composition of boar Duroc, Yorkshire, Landrace and Hampshire pigs
Yingping Xiao, Kaifeng Li, Yun Xiang, Weidong Zhou, Guohong Gui, Hua Yang
Asian-Australasian Journal of Animal Sciences.2017; 30(10): 1456. CrossRef
Gut microbiota can transfer fiber characteristics and lipid metabolic profiles of skeletal muscle from pigs to germ-free mice
Honglin Yan, Hui Diao, Yi Xiao, Wenxia Li, Bing Yu, Jun He, Jie Yu, Ping Zheng, Xiangbing Mao, Yuheng Luo, Benhua Zeng, Hong Wei, Daiwen Chen
Scientific Reports.2016;[Epub] CrossRef
Intestinal microbiota could transfer host Gut characteristics from pigs to mice
H. Diao, H. L. Yan, Y. Xiao, B. Yu, J. Yu, J. He, P. Zheng, B.H. Zeng, H. Wei, X.B. Mao, D.W. Chen
BMC Microbiology.2016;[Epub] CrossRef
The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water
Abhilasha Karkey, Thibaut Jombart, Alan W. Walker, Corinne N. Thompson, Andres Torres, Sabina Dongol, Nga Tran Vu Thieu, Duy Pham Thanh, Dung Tran Thi Ngoc, Phat Voong Vinh, Andrew C. Singer, Julian Parkhill, Guy Thwaites, Buddha Basnyat, Neil Ferguson, S
PLOS Neglected Tropical Diseases.2016; 10(1): e0004346. CrossRef
Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing
Jong Pyo Chae, Edward Alain B. Pajarillo, Ju Kyoung Oh, Heebal Kim, Dae‐Kyung Kang
Microbial Biotechnology.2016; 9(4): 486. CrossRef
Effect of sodium humate and zinc oxide used in prophylaxis of post-weaning diarrhoea on faecal microbiota composition in weaned piglets
M. Kaevska, A. Lorencova, P. Videnska, K. Sedlar, I. Provaznik, M. Trckova
Veterinární medicína.2016; 61(6): 328. CrossRef
Changes in the diversity and composition of gut microbiota of weaned piglets after oral administration of Lactobacillus or an antibiotic
Dongyan Zhang, Haifeng Ji, Hui Liu, Sixin Wang, Jing Wang, Yamin Wang
Applied Microbiology and Biotechnology.2016; 100(23): 10081. CrossRef
Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)
Klára Vlčková, Andres Gomez, Klára J. Petrželková, Christopher A. Whittier, Angelique F. Todd, Carl J. Yeoman, Karen E. Nelson, Brenda A. Wilson, Rebecca M. Stumpf, David Modrý, Bryan A. White, Steven R. Leigh
Microbial Ecology.2016; 72(4): 943. CrossRef
N2 Gas Flushing Alleviates the Loss of Bacterial Diversity and Inhibits Psychrotrophic Pseudomonas during the Cold Storage of Bovine Raw Milk
Silvia Gschwendtner, Tapani Alatossava, Susanne Kublik, Mirna Mrkonjić Fuka, Michael Schloter, Patricia Munsch-Alatossava, George-John Nychas
PLOS ONE.2016; 11(1): e0146015. CrossRef
Effects of dispersal limitation in the face of intense selection via dietary intervention on the faecal microbiota of rats
Heli J. Barron Pastor, David M. Gordon
Environmental Microbiology Reports.2016; 8(2): 187. CrossRef
Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
Katharina Burbach, Jana Seifert, Dietmar H. Pieper, Amélia Camarinha‐Silva
MicrobiologyOpen.2016; 5(1): 70. CrossRef
Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits
Brigita Nograšek, Tomaž Accetto, Lijana Fanedl, Gorazd Avguštin
Journal of Microbiology.2015; 53(8): 503. CrossRef
A comparison of faecal microbial populations of South African Windsnyer-type indigenous pigs (SAWIPs) and Large White × Landrace (LW × LR) crosses fed diets containing ensiled maize cobs
Arnold T. Kanengoni, Michael Chimonyo, Taurai Tasara, Paul Cormican, Aspinas Chapwanya, Bongani K. Ndimba, Kennedy Dzama, Abelardo Margolles
FEMS Microbiology Letters.2015; 362(13): fnv100. CrossRef
Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing
Edward Alain B. Pajarillo, Jong Pyo Chae, Marilen P. Balolong, Hyeun Bum Kim, Kang-Seok Seo, Dae-Kyung Kang
Asian-Australasian Journal of Animal Sciences.2015; 28(4): 584. CrossRef
Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation
Edward Alain B. Pajarillo, Jong Pyo Chae, Hyeun Bum Kim, In Ho Kim, Dae-Kyung Kang
Applied Microbiology and Biotechnology.2015; 99(13): 5647. CrossRef
The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing
Hyeun Bum Kim, Richard E. Isaacson
Veterinary Microbiology.2015; 177(3-4): 242. CrossRef
Effects of probiotic Enterococcus faecium NCIMB 11181 administration on swine fecal microbiota diversity and composition using barcoded pyrosequencing
Edward Alain B. Pajarillo, Jong Pyo Chae, Marilen P. Balolong, Hyeun Bum Kim, Chan-Soo Park, Dae-Kyung Kang
Animal Feed Science and Technology.2015; 201: 80. CrossRef
Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing
Jong Pyo Chae, Edward Alain B. Pajarillo, Chan-Soo Park, Dae-Kyung Kang
Animal Feed Science and Technology.2015; 209: 157. CrossRef

Bacillus daqingensis sp. nov., a Halophilic, Alkaliphilic Bacterium Isolated from Saline-Sodic Soil in Daqing, China: Shuang Wang , Lei Sun , Dan Wei , Baoku Zhou , Junzheng Zhang , Xuejia Gu , Lei Zhang , Ying Liu , Yidan Li , Wei Guo , Shuang Jiang , Yaqing Pan , Yufeng Wang; J. Microbiol. 2014;52(7):548-553. Published online May 30, 2014; DOI: https://doi.org/10.1007/s12275-014-3376-x

430 View
0 Download
7 Crossref

Abstract PDF

An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1T, was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1T was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0–16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5–11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1T is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402T (97.8% similarity) and B. agaradhaerens DSM 8721T (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1T represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1T (=NBRC 109404T =CGMCC 1.12295T).

Citations

Citations to this article as recorded by

Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Alteribacter salitolerans sp. nov., isolated from a saline-alkaline soil
Shuang Wang, Lei Sun, Manik Prabhu Narsing Rao, Guo-Hong Liu, Pin-Jiao Jin, Zhou-Yan Dong, Zheng-Han Lian, Xiao-Yu Hao, Ming-Yi Zhang, Wen-Jun Li
Archives of Microbiology.2022;[Epub] CrossRef
Microbial Diversity and Adaptation under Salt-Affected Soils: A Review
Chiranjeev Kumawat, Ajay Kumar, Jagdish Parshad, Shyam Sunder Sharma, Abhik Patra, Prerna Dogra, Govind Kumar Yadav, Sunil Kumar Dadhich, Rajhans Verma, Girdhari Lal Kumawat
Sustainability.2022; 14(15): 9280. CrossRef
Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain
Shuang Wang, Lei Sun, Ning Ling, Chen Zhu, Fengqin Chi, Weiqun Li, Xiaoyu Hao, Wu Zhang, Jingyang Bian, Lei Chen, Dan Wei
Frontiers in Microbiology.2020;[Epub] CrossRef
Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake
Baisuo Zhao, Weidong Lu, Shanshan Zhang, Kang Liu, Yanchun Yan, Jun Li
International Journal of Systematic and Evolutionary Microbiology.2017; 67(5): 1557. CrossRef
Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake
Shanshan Zhang, Zhaojun Li, Yanchun Yan, Chuanlun Zhang, Jun Li, Baisuo Zhao
International Journal of Systematic and Evolutionary Microbiology.2016; 66(6): 2305. CrossRef
Microbially-driven strategies for bioremediation of bauxite residue
Talitha C. Santini, Janice L. Kerr, Lesley A. Warren
Journal of Hazardous Materials.2015; 293: 131. CrossRef

Profiling of the Bacteria Responsible for Pyogenic Liver Abscess by 16S rRNA Gene Pyrosequencing: Yun Gyu Song , Sang Gun Shim , Kwang Min Kim , Dong-Hae Lee , Dae-Soo Kim , Sang-Haeng Choi , Jae-Young Song , Hyung-Lyun Kang , Seung-Chul Baik , Woo-Kon Lee , Myung-Je Cho , Kwang-Ho Rhee; J. Microbiol. 2014;52(6):504-509. Published online May 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4241-7

367 View
0 Download
24 Crossref

Abstract PDF

Pyogenic liver abscess (PLA) is a severe disease with considerable mortality and is often polymicrobial. Understanding the pathogens that cause PLA is the basis for PLA treatment. Here, we profiled the bacterial composition in PLA fluid by pyrosequencing the 16S ribosomal RNA (rRNA) gene based on next-generation sequencing (NGS) technology to identify etiological agents of PLA and to provide information of their 16S rRNA sequences for application to DNA-based techniques in the hospital. Twenty patients with PLA who underwent percutaneous catheter drainage, abscess culture, and blood culture for isolates were included. Genomic DNAs from abscess fluids were subjected to polymerase chain reaction and pyrosequencing of the 16S rRNA gene with a 454 GS Junior System. The abscess and blood cultures were positive in nine (45%) and four (20%) patients, respectively. Pyrosequencing of 16S rRNA gene showed that 90% of the PLA fluid samples contained single or multiple genera of known bacteria such as Klebsiella, Fusobacterium, Streptococcus, Bacteroides, Prevotella, Peptostreptococcus, unassigned Enterobacteriaceae, and Dialister. Klebsiella was predominantly found in the PLA fluid samples. All samples that carried unassigned bacteria had 26.8% reads on average. We demonstrated that the occurrence of PLA was associated with eight known bacterial genera as well as unassigned bacteria and that 16S rRNA gene sequencing was more useful than conventional culture methods for accurate identification of bacterial pathogens from PLA.

Citations

Citations to this article as recorded by

Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods
Verónica Fernández-Sánchez, Estibeyesbo Said Plascencia-Nieto, Mónica Alethia Cureño-Díaz, Emilio Mariano Durán-Manuel, Aida Verónica Rodríguez-Tovar, Claudia Camelia Calzada-Mendoza, Clemente Cruz-Cruz, Miguel Ángel Loyola-Cruz, María Elizbeth Álvarez-Sá
Microorganisms.2025; 13(1): 131. CrossRef
Pyogenic liver abscess and sepsis caused by mixed anaerobic bacteria in an immunocompetent adult: a case report
Ziwen Fan, Mu Mei, Cen Chen
Frontiers in Medicine.2025;[Epub] CrossRef
Alterations of Gut Microbiota in Pyogenic Liver Abscess Patients with and without Type 2 Diabetes Mellitus
Shanshan Liu, Xiaomeng Ge, Xizhan Xu, Kang Zhang, Xinxin Lu
Infection and Drug Resistance.2024; Volume 17: 2149. CrossRef
Absceso hepático
G. Rossi, M. Ronot, V. Zarrouk, A. Lefort
EMC - Tratado de Medicina.2024; 28(3): 1. CrossRef
Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus
Yawen Guo, Hairui Wang, Zhaoyu Liu, Zhihui Chang
Frontiers in Microbiology.2023;[Epub] CrossRef
Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses
Zhijie Zhang, Hairui Wang, Yawen Guo, Zhaoyu Liu, Zhihui Chang
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Involvement of Fusobacterium nucleatum in malignancies except for colorectal cancer: A literature review
Zhixing He, Wei Tian, Qichun Wei, Jing Xu
Frontiers in Immunology.2022;[Epub] CrossRef
Liver abscesses in the Western pediatric population
L Grossar, I Hoffman, E Sokal, X Stéphenne, P Witters
Acta Gastro Enterologica Belgica.2022; 85(3): 439. CrossRef
Characterization of abscesses from liver, pancreas and kidney using deep sequencing of the 16S rRNA gene
Joanna Małgorzata Bivand, Randi Monsen Nygaard, Øyvind Kommedal
Diagnostic Microbiology and Infectious Disease.2021; 99(3): 115277. CrossRef
Brevundimonas diminutacoinfection as source of pyogenic liver abscess
Jacob Burch, Shilpa Tatineni, Ikponmwosa Enofe, Heather Laird-Fick
BMJ Case Reports.2021; 14(5): e236235. CrossRef
Real‐time PCR versus MALDI‐TOF MS and culture‐based techniques for diagnosis of bloodstream and pyogenic infections in humans and animals
N.K. Abd El‐Aziz, A.A Gharib, E.A.A. Mohamed, A.H. Hussein
Journal of Applied Microbiology.2021; 130(5): 1630. CrossRef
Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers
Joe Jongpyo Lim, Moumita Dutta, Joseph L Dempsey, Hans-Joachim Lehmler, James MacDonald, Theo Bammler, Cheryl Walker, Terrance J Kavanagh, Haiwei Gu, Sridhar Mani, Julia Yue Cui
Toxicological Sciences.2021; 184(1): 83. CrossRef
Impact of Qualitative and Quantitative Biliary Contamination Status on the Incidence of Postoperative Infection Complications in Patients Undergoing Pancreatoduodenectomy
Masaya Suenaga, Yukihiro Yokoyama, Tsutomu Fujii, Suguru Yamada, Junpei Yamaguchi, Masamichi Hayashi, Takashi Asahara, Masato Nagino, Yasuhiro Kodera
Annals of Surgical Oncology.2021; 28(1): 560. CrossRef
Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota
Kavita Agarwal, Lloyd S. Robinson, Somya Aggarwal, Lynne R. Foster, Ariel Hernandez-Leyva, Hueylie Lin, Brett A. Tortelli, Valerie P. O’Brien, Liza Miller, Andrew L. Kau, Hilary Reno, Nicole M. Gilbert, Warren G. Lewis, Amanda L. Lewis, Ken Cadwell
PLOS Biology.2020; 18(8): e3000788. CrossRef
Clinical characteristics and treatment outcomes in a cohort of patients with pyogenic and amoebic liver abscess
Lorna Neill, Frances Edwards, Simon M. Collin, David Harrington, Dominic Wakerley, Guduru Gopal Rao, Alastair C. McGregor
BMC Infectious Diseases.2019;[Epub] CrossRef
Profiling of the Causative Bacteria in Infected Lymphocysts after Lymphadenectomy for Gynecologic Cancer by Pyrosequencing the 16S Ribosomal RNA Gene Using Next-Generation Sequencing Technology
Yuya Nogami, Kouji Banno, Masataka Adachi, Haruko Kunitomi, Yusuke Kobayashi, Eiichiro Tominaga, Daisuke Aoki
Infectious Diseases in Obstetrics and Gynecology.2019; 2019: 1. CrossRef
PCR Characterization of Microbiota on Contracted and Non-Contracted Breast Capsules
Yara Bachour, Linda Poort, Stephan P. Verweij, Gijs van Selms, Hay A. H. Winters, Marco J. P. F. Ritt, Frank B. Niessen, Andries E. Budding
Aesthetic Plastic Surgery.2019; 43(4): 918. CrossRef
Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study
Ken-ichi Okuda, Yutaka Yoshii, Satomi Yamada, Akio Chiba, Ippei Hironaka, Seiji Hori, Katsuhiko Yanaga, Yoshimitsu Mizunoe
Annals of Clinical Microbiology and Antimicrobials.2018;[Epub] CrossRef
Rapid Communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States1
M. D. Weinroth, C. R. Carlson, J. N. Martin, J. L. Metcalf, P. S. Morley, K. E. Belk
Journal of Animal Science.2017; 95(10): 4520. CrossRef
Fusobacterium nucleatum in gastroenterological cancer: Evaluation of measurement methods using quantitative polymerase chain reaction and a literature review
Kensuke Yamamura, Yoshifumi Baba, Keisuke Miyake, Kenichi Nakamura, Hironobu Shigaki, Kosuke Mima, Junji Kurashige, Takatsugu Ishimoto, Masaaki Iwatsuki, Yasuo Sakamoto, Yoichi Yamashita, Naoya Yoshida, Masayuki Watanabe, Hideo Baba
Oncology Letters.2017;[Epub] CrossRef
Fusobacterial liver abscess: a case report and review of the literature
Dilip Jayasimhan, Linus Wu, Paul Huggan
BMC Infectious Diseases.2017;[Epub] CrossRef
Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples
Andries E. Budding, Martine Hoogewerf, Christina M. J. E. Vandenbroucke-Grauls, Paul H. M. Savelkoul, N. A. Ledeboer
Journal of Clinical Microbiology.2016; 54(4): 934. CrossRef
Fusobacterium nucleatum infections: clinical spectrum and bacteriological features of 78 cases
E. Denes, O. Barraud
Infection.2016; 44(4): 475. CrossRef
Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines
Edward Alain B. Pajarillo, Jong Pyo Chae, Marilen P. Balolong, Hyeun Bum Kim, Kang-Seok Seo, Dae-Kyung Kang
Journal of Microbiology.2014; 52(8): 646. CrossRef

Assessment of Microbial Diversity Bias Associated with Soil Heterogeneity and Sequencing Resolution in Pyrosequencing Analyses: Sokhee P. Jung , Hojeong Kang; J. Microbiol. 2014;52(7):574-580. Published online May 13, 2014; DOI: https://doi.org/10.1007/s12275-014-3636-9

326 View
0 Download
10 Crossref

Abstract PDF

It is important to estimate the true microbial diversities accurately for a comparative microbial diversity analysis among various ecological settings in ecological models. Despite drastically increasing amounts of 16S rRNA gene targeting pyrosequencing data, sampling and data interpretation for comparative analysis have not yet been standardized. For more accurate bacterial diversity analyses, the influences of soil heterogeneity and sequence resolution on bacterial diversity estimates were investigated using pyrosequencing data of oak and pine forest soils with focus on the bacterial 16S rRNA gene. Soil bacterial community sets were phylogenetically clustered into two separate groups by forest type. Rarefaction curves showed that bacterial communities sequenced from the DNA mixtures and the DNAs of the soil mixtures had midsize richness compared with other samples. Richness and diversity estimates were highly variable depending on the sequence read numbers. Bacterial richness estimates (ACE, Chao 1 and Jack) of the forest soils had positive linear relationships with the sequence read number. Bacterial diversity estimates NPShannon, Shannon and the inverse Simpson) of the forest soils were also positively correlated with the sequence read number. One-way ANOVA shows that sequence resolution significantly affected the α-diversity indices (P<0.05), but the soil heterogeneity did not (P>0.05). For an unbiased evaluation, richness and diversity estimates should be calculated and compared from subsets of the same size.

Citations

Citations to this article as recorded by

Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake
Daoyuan Li, Hengsheng Wang, Naidong Chen, Haiyang Jiang, Naifu Chen
Brazilian Journal of Microbiology.2024; 55(3): 2423. CrossRef
Characterization of pollutants and identification of microbial communities in the filter media of green infrastructures
H.S. Choi, Nash Jett Reyes, Minsu Jeon, L.H. Kim
Ecological Engineering.2023; 193: 107012. CrossRef
Effects of Hydroxy-Alpha-Sanshool on Intestinal Metabolism in Insulin-Resistant Mice
Fangyan Xu, Yuping Zhu, Mintao Lu, Likang Qin, Degang Zhao, Tingyuan Ren
Foods.2022; 11(14): 2040. CrossRef
Trends and Prospects of Sediment Microbial Fuel Cells as Sustainable Aquatic Ecosystem Remediation Technology
Sunghoon Son, Sokhee P. Jung
Journal of Korean Society of Environmental Engineers.2022; 44(11): 468. CrossRef
Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34
Wimonrat Panpetch, Pratsanee Hiengrach, Sumanee Nilgate, Somying Tumwasorn, Naraporn Somboonna, Alisa Wilantho, Piraya Chatthanathon, Piyapan Prueksapanich, Asada Leelahavanichkul
Gut Microbes.2020; 11(3): 465. CrossRef
Roxithromycin regulates intestinal microbiota and alters colonic epithelial gene expression
Cheng Zhang, Xuanwei Li, Liu Liu, Lijuan Gao, Shiyi Ou, Jianming Luo, Xichun Peng
Applied Microbiology and Biotechnology.2018; 102(21): 9303. CrossRef
Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts
Ashagrie Gibtan, Kyounghee Park, Mingyeong Woo, Jung-Kue Shin, Dong-Woo Lee, Jae Hak Sohn, Minjung Song, Seong Woon Roh, Sang-Jae Lee, Han-Seung Lee
Frontiers in Microbiology.2017;[Epub] CrossRef
Detecting macroecological patterns in bacterial communities across independent studies of global soils
Kelly S. Ramirez, Christopher G. Knight, Mattias de Hollander, Francis Q. Brearley, Bede Constantinides, Anne Cotton, Si Creer, Thomas W. Crowther, John Davison, Manuel Delgado-Baquerizo, Ellen Dorrepaal, David R. Elliott, Graeme Fox, Robert I. Griffiths,
Nature Microbiology.2017; 3(2): 189. CrossRef
Assessment on cadmium and lead in soil based on a rhizosphere microbial community
Xu Zhang, Huanhuan Yang, Zhaojie Cui
Toxicology Research.2017; 6(5): 671. CrossRef
The analysis of clonal expansions in normal and autoimmune B cell repertoires
Uri Hershberg, Eline T. Luning Prak
Philosophical Transactions of the Royal Society B: Biological Sciences.2015; 370(1676): 20140239. CrossRef

Variations in 16S rRNA-based Microbiome Profiling between Pyrosequencing Runs and between Pyrosequencing Facilities: Minseok Kim , Zhongtang Yu; J. Microbiol. 2014;52(5):355-365. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3443-3

317 View
0 Download
32 Crossref

Abstract PDF

Pyrosequencing of 16S rRNA gene amplicons on the 454 FLX Titanium platform has been widely used to analyze microbiomes in various environments. However, different results may stem from variations among sequencing runs or among sequencing facilities. This study aimed to evaluate these variations between different pyrosequencing runs by sequencing 16S rRNA gene amplicon libraries generated from three sets of rumen samples twice each on the 454 FLX Titanium system at two independent sequencing facilities. Similar relative abundances were found for predominant taxa represented by large numbers of sequence reads but not for minor taxa represented by small numbers of sequence reads. The two sequencing facilities revealed different bac-terial profiles with respect to both predominant taxa and minor taxa, including the most predominant genus Prevo-tella, the family Lachnospiraceae, and the phylum Proteo-bacteria. Differences in primers used to generate amplicon libraries may be a major source of variations in microbiome profiling. Because different primers and regions of 16S rRNA genes are often used by different researchers, significant variations likely exist among studies. Quantitative interpre-tation for relative abundance of taxa, especially minor taxa, from prevalence of sequence reads and comparisons of re-sults from different studies should be done with caution.

Citations

Citations to this article as recorded by

Analysis of Alterations in Intestinal Flora in Chinese Elderly with Cardiovascular Disease and Its Association with Trimethylamine
Yannan He, Song Chen, Yuling Xue, Han Lu, Ziteng Li, Xianxian Jia, Yibing Ning, Qingbin Yuan, Shijie Wang
Nutrients.2024; 16(12): 1864. CrossRef
The association between the respiratory tract microbiome and clinical outcomes in patients with COPD
Suyun Yu, Huiping Zhang, Liping Wan, Min Xue, Yunfeng Zhang, Xiwen Gao
Microbiological Research.2023; 266: 127244. CrossRef
SVep1, a temperate phage of human oral commensal Streptococcus vestibularis
Miaomiao Wu, Yanpeng Zhu, Yuhui Yang, Yali Gong, Zongyue Chen, Binyou Liao, Yu Xiong, Xia Zhou, Yan Li
Frontiers in Microbiology.2023;[Epub] CrossRef
Influence of dietary organic trace minerals on enteric methane emissions and rumen microbiota of heat-stressed dairy steers
A-Rang Son, Mahfuzul Islam, Seon-Ho Kim, Sung-Sill Lee, Sang-Suk Lee
Journal of Animal Science and Technology.2023; 65(1): 132. CrossRef
Gut microbiota is a potential goalkeeper of dyslipidemia
Lirong Lei, Ning Zhao, Lei Zhang, Jiamei Chen, Xiaomin Liu, Shenghua Piao
Frontiers in Endocrinology.2022;[Epub] CrossRef
Analyzing the Complicated Connection Between Intestinal Microbiota and Cardiovascular Diseases
Tanishq Kumar, Rajoshee R Dutta, Vivek R Velagala, Benumadhab Ghosh, Abhay Mudey
Cureus.2022;[Epub] CrossRef
Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration
Mahfuzul Islam, Seon-Ho Kim, A-Rang Son, Sonny C. Ramos, Chang-Dae Jeong, Zhongtang Yu, Seung Ha Kang, Yong-Il Cho, Sung-Sill Lee, Kwang-Keun Cho, Sang-Suk Lee
Animals.2021; 11(4): 1184. CrossRef
Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages
Lucia Bailoni, Lisa Carraro, Marco Cardin, Barbara Cardazzo
Microorganisms.2021; 9(4): 754. CrossRef
Holstein and Jersey Steers Differ in Rumen Microbiota and Enteric Methane Emissions Even Fed the Same Total Mixed Ration
Mahfuzul Islam, Seon-Ho Kim, Sonny C. Ramos, Lovelia L. Mamuad, A-Rang Son, Zhongtang Yu, Sung-Sil Lee, Yong-Il Cho, Sang-Suk Lee
Frontiers in Microbiology.2021;[Epub] CrossRef
Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits
Ming-Yuan Xue, Yun-Yi Xie, Yi-Fan Zhong, Jian-Xin Liu, Le Luo Guan, Hui-Zeng Sun
Animal Microbiome.2021;[Epub] CrossRef
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle
Fuyong Li, Changxi Li, Yanhong Chen, Junhong Liu, Chunyan Zhang, Barry Irving, Carolyn Fitzsimmons, Graham Plastow, Le Luo Guan
Microbiome.2019;[Epub] CrossRef
Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants
R.J. Gruninger, G.O. Ribeiro, A. Cameron, T.A. McAllister
Animal.2019; 13(9): 1843. CrossRef
Testing culture purity in prokaryotes: criteria and challenges
Alexander V. Pinevich, Eugeny E. Andronov, Elizaveta V. Pershina, Agnia A. Pinevich, Helena Y. Dmitrieva
Antonie van Leeuwenhoek.2018; 111(9): 1509. CrossRef
Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile
Filippo Biscarini, Fiorentina Palazzo, Federica Castellani, Giulia Masetti, Lisa Grotta, Angelo Cichelli, Giuseppe Martino, Juan J Loor
PLOS ONE.2018; 13(11): e0205670. CrossRef
Ruminal methane emissions, metabolic, and microbial profile of Holstein steers fed forage and concentrate, separately or as a total mixed ration
Rajaraman Bharanidharan, Selvaraj Arokiyaraj, Eun Bae Kim, Chang Hyun Lee, Yang Won Woo, Youngjun Na, Danil Kim, Kyoung Hoon Kim, Alex V. Chaves
PLOS ONE.2018; 13(8): e0202446. CrossRef
Investigation of the core microbiome in main soil types from the East European plain
Elizaveta V. Pershina, Ekaterina A. Ivanova, Ilia O. Korvigo, Evgeny L. Chirak, Nurlan H. Sergaliev, Evgeny V. Abakumov, Nikolai A. Provorov, Evgeny E. Andronov
Science of The Total Environment.2018; 631-632: 1421. CrossRef
Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation
Thomas Hartinger, Nina Gresner, Karl-Heinz Südekum
Journal of Animal Science and Biotechnology.2018;[Epub] CrossRef
Assessment of Rumen Microbiota from a Large Dairy Cattle Cohort Reveals the Pan and Core Bacteriomes Contributing to Varied Phenotypes
Mingyuan Xue, Huizeng Sun, Xuehui Wu, Le Luo Guan, Jianxin Liu, Hideaki Nojiri
Applied and Environmental Microbiology.2018;[Epub] CrossRef
Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle
Fuyong Li, Le Luo Guan, Andrew J. McBain
Applied and Environmental Microbiology.2017;[Epub] CrossRef
Impact of micro‐environmental changes on respiratory tract infections with intracellular bacteria
Kensuke Shima, Jonas Coopmeiners, Simon Graspeuntner, Klaus Dalhoff, Jan Rupp
FEBS Letters.2016; 590(21): 3887. CrossRef
Diversity at low abundance: The phenomenon of the rare bacterial biosphere
M. Yu. Skopina, A. A. Vasileva, E. V. Pershina, A. V. Pinevich
Microbiology.2016; 85(3): 272. CrossRef
Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens
Lingling Wang, Mike Lilburn, Zhongtang Yu
Frontiers in Microbiology.2016;[Epub] CrossRef
Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches
Fuyong Li, Gemma Henderson, Xu Sun, Faith Cox, Peter H. Janssen, Le Luo Guan
Frontiers in Microbiology.2016;[Epub] CrossRef
The Bacteriomes of Ileal Mucosa and Cecal Content of Broiler Chickens and Turkeys as Revealed by Metagenomic Analysis
Shan Wei, Michael Lilburn, Zhongtang Yu
International Journal of Microbiology.2016; 2016: 1. CrossRef
Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy
Ting Luo, Usha Srinivasan, Kirtana Ramadugu, Kerby A. Shedden, Katherine Neiswanger, Erika Trumble, Jiean J. Li, Daniel W. McNeil, Richard J. Crout, Robert J. Weyant, Mary L. Marazita, Betsy Foxman, S.-J. Liu
Applied and Environmental Microbiology.2016; 82(18): 5519. CrossRef
The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline
Jérôme Lluch, Florence Servant, Sandrine Païssé, Carine Valle, Sophie Valière, Claire Kuchly, Gaëlle Vilchez, Cécile Donnadieu, Michael Courtney, Rémy Burcelin, Jacques Amar, Olivier Bouchez, Benjamin Lelouvier, Markus M. Heimesaat
PLOS ONE.2015; 10(11): e0142334. CrossRef
RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis1,2,3
T. A. McAllister, S. J. Meale, E. Valle, L. L. Guan, M. Zhou, W. J. Kelly, G. Henderson, G. T. Attwood, P. H. Janssen
Journal of Animal Science.2015; 93(4): 1431. CrossRef
Library preparation methodology can influence genomic and functional predictions in human microbiome research
Marcus B. Jones, Sarah K. Highlander, Ericka L. Anderson, Weizhong Li, Mark Dayrit, Niels Klitgord, Martin M. Fabani, Victor Seguritan, Jessica Green, David T. Pride, Shibu Yooseph, William Biggs, Karen E. Nelson, J. Craig Venter
Proceedings of the National Academy of Sciences.2015; 112(45): 14024. CrossRef
Role of the normal gut microbiota
Sai Manasa Jandhyala
World Journal of Gastroenterology.2015; 21(29): 8787. CrossRef
RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition1,2
J. L. Firkins, Z. Yu
Journal of Animal Science.2015; 93(4): 1450. CrossRef
Effect of Haylage and Monensin Supplementation on Ruminal Bacterial Communities of Feedlot Cattle
Minseok Kim, Tara L. Felix, Steve C. Loerch, Zhongtang Yu
Current Microbiology.2014; 69(2): 169. CrossRef
Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities
M. Kim, L. Wang, M. Morrison, Z. Yu
Journal of Applied Microbiology.2014; 117(4): 949. CrossRef

NOTE] Pedobacter soyangensis sp. nov., Isolated from Lake Soyang in Korea: Yochan Joung , Heeyoung Kang , Haneul Kim , Beom-Il Lee , O-Seob Kwon , Kiseong Joh; J. Microbiol. 2014;52(1):83-87. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3284-0

349 View
1 Download
4 Crossref

Abstract PDF

Strain HME6451T was isolated from Lake Soyang in Korea. Phylogenetic tree based on 16S rRNA gene sequence showed that strain HME6451T formed a lineage within the genus Pedobacter. The strain HME6451T was closely related to Pedobacter daechungensis (95.4% sequence similarity), Pedobacter lentus (94.4%), and Pedobacter glucosidilyticus (93.8%). And strain HME6451T was a Gram-staining-negative, short rodshaped, strictly aerobic bacterium. The major fatty acids were iso-C15:0 (41.2%), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 23.1%), and iso-C17:0-3OH (10.1%). The polar lipids of HME6451T were consisted of one phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content was 36.0 mol%. On the basis of the evidence presented in this study, strain HME6451T represent a novel species of the genus Pedobacter, for which the name Pedobacter soyangensis sp. nov., is proposed the type strain HME6451T (=KCTC 23467T =CECT 7865T).

Citations

Citations to this article as recorded by

Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica
Peter Kämpfer, Rute Irgang, Guillermo Fernández-Negrete, Hans-Jürgen Busse, Matías Poblete-Morales, Derie Fuentes-Messina, Stefanie P. Glaeser, Ruben Avendaño-Herrera
Antonie van Leeuwenhoek.2019; 112(10): 1465. CrossRef
Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine
Zhiyong Wang, Yuanqing Tan, Ding Xu, Gejiao Wang, Jihong Yuan, Shixue Zheng
International Journal of Systematic and Evolutionary Microbiology.2016; 66(12): 5112. CrossRef
Pedobacter rivuli sp. nov., isolated from a freshwater stream
Heeyoung Kang, Haneul Kim, Yochan Joung, Kiseong Joh
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_12): 4073. CrossRef

Sunxiuqinia dokdonensis sp. nov., Isolated from Deep Sub-Seafloor Sediment: Dong-Ho Chang , Jae-Bong Lee , Geun-Hye Lee , Moon-Soo Rhee , Haewon Lee , Kyung Sook Bae , Doo-Sang Park , Byoung-Chan Kim; J. Microbiol. 2013;51(6):741-746. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3492-z

456 View
0 Download
10 Crossref

Abstract PDF

A novel facultatively anaerobic strain DH1T was isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea. The new strain was characterized using polyphasic approaches. The isolate was Gram-stain-negative, motile by gliding, non-spore-forming rods, oxidase-negative, and catalase-positive; and formed colonies of orange-red color. The NaCl range for growth was 0.5–7.0% (w/v) and no growth was observed in the absence of NaCl. The isolate grew optimally at 30°C, with 2% (w/v) NaCl and at pH 7. The cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 40.8 mol%. The closest related strains are Sunxiuqinia faeciviva JAM-BA0302T and Sunxiuqinia elliptica DQHS-4T (97.9 and 96.3% sequence similarity, respectively). The level of DNADNA relatedness between strain DH1T and S. faeciviva JAMBA0302T was around 41% (but only 6% between DH1T and S. elliptica DQHS-4T). The major cellular fatty acids of the isolate were contained iso-C15:0 (25.9%), anteiso-C15:0 (16.7%), and summed feature 9 (comprising C16:0 3-OH and/or unknown fatty acid of dimethylacetal ECL 17.157; 13.2%). The predominant menaquinone was MK-7. On the basis of polyphasic evidence from this study, the isolate was considered to represent a novel species of the genus Sunxiuqinia, for which the name Sunxiuqinia dokdonensis sp. nov. is proposed; the type strain is DH1T (=KCTC 32503T =CGMCC 1.12676T =JCM 19380T).

Citations

Citations to this article as recorded by

Gaoshiqia hydrogeniformans sp. nov., a novel hydrogen-producing bacterium isolated from a deep diatomaceous shale formation
Akio Ueno, Kiyoshi Sato, Shuji Tamamura, Takuma Murakami, Hidenori Inomata, Satoshi Tamazawa, Yuki Amano, Kazuya Miyakawa, Takeshi Naganuma, Toshifumi Igarashi
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Deltaproteobacterium Strain KaireiS1, a Mesophilic, Hydrogen-Oxidizing and Sulfate-Reducing Bacterium From an Inactive Deep-Sea Hydrothermal Chimney
Nicole Adam, Yuchen Han, Katja Laufer-Meiser, Rebecca Bährle, Ulrich Schwarz-Schampera, Axel Schippers, Mirjam Perner
Frontiers in Microbiology.2021;[Epub] CrossRef
Sunxiuqinia indica sp. nov., isolated from deep sea
Jianyang Li, Mingming Qi, Qiliang Lai, Guangyi Wang, Zongze Shao
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4186. CrossRef
Description of Maribellus sediminis sp. nov., a marine nitrogen-fixing bacterium isolated from sediment of cordgrass and mangrove
Zhaobin Huang, Yuzhong Hu, Qiliang Lai, Yu Guo
Systematic and Applied Microbiology.2020; 43(4): 126099. CrossRef
Simulated reactive zone with emulsified vegetable oil for the long-term remediation of Cr(VI)-contaminated aquifer: dynamic evolution of geological parameters and groundwater microbial community
Jun Dong, Jinqiu Yu, Qiburi Bao
Environmental Science and Pollution Research.2018; 25(34): 34392. CrossRef
Whole-genome sequence of Sunxiuqinia dokdonensis DH1 T , isolated from deep sub-seafloor sediment in Dokdo Island
Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim
Genomics Data.2016; 9: 95. CrossRef
The composition, localization and function of low-temperature-adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils
Y. Dai, Z. Yan, L. Jia, S. Zhang, L. Gao, X. Wei, Z. Mei, X. Liu
Journal of Applied Microbiology.2016; 121(1): 163. CrossRef
Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment
Wen-Jie Wu, Qian-Qian Liu, Guan-Jun Chen, Zong-Jun Du
International Journal of Systematic and Evolutionary Microbiology .2015; 65(Pt_7): 2260. CrossRef
Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae)
Byung-Ho Bang, Moon-Soo Rhee, Dong-Ho Chang, Doo-Sang Park, Byoung-Chan Kim
Antonie van Leeuwenhoek.2015; 107(2): 443. CrossRef
Bacterial colonization of a fumigated alkaline saline soil
Juan M. Bello-López, Cristina A. Domínguez-Mendoza, Arit S. de León-Lorenzana, Laura Delgado-Balbuena, Yendi E. Navarro-Noya, Selene Gómez-Acata, Analine Rodríguez-Valentín, Victor M. Ruíz-Valdiviezo, Marco Luna-Guido, Nele Verhulst, Bram Govaerts, Luc De
Extremophiles.2014; 18(4): 733. CrossRef

NOTE] Pontibacter jeungdoensis sp. nov., Isolated from a Solar Saltern in Korea: Yochan Joung , Haneul Kim , Beom-Il Lee , Heeyoung Kang , Tae Yong Jang , O-Seob Kwon , Kiseong Joh; J. Microbiol. 2013;51(4):531-535. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2324-5

241 View
0 Download
12 Crossref

Abstract PDF

A Gram-staining-negative, rod-shaped and red-pigmented bacterial strain, HMD3125T, was isolated from a solar saltern in Jeungdo, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3125T formed a lineage within the genus Pontibacter and was similar to Pontibacter salisaro (96.1%) and P. korlensis (95.3%). The major fatty acids of strain HMD3125T were summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B; 30.4%), iso-C15:0 (20.4%) and iso-C17:0 3OH (17.2%). The polar lipid profile of HMD3125T consisted of the phosphatidylethanolamine, four unidentified polar lipids, unidentified phospholipid, unidentified aminolipid and unidentified aminophospholipid. Strain HMD3125T contained MK-7 as the predominant menaquinone and sym-homospermidine as the major polyamine. The DNA G+C content of strain HMD3125T was 45.6 mol%. Strain HMD3125T assigned as a novel species in the genus Pontibacter, for which the name Pontibacter jeungdoensis sp. nov. is proposed. The type strain is HMD3125T (=KCTC 23156T =CECT 7710T).

Citations

Citations to this article as recorded by

Microbial community and functional prediction during the processing of salt production in a 1000-year-old marine solar saltern of South China
Ya-Li Wei, Zi-Jie Long, Ming-Xun Ren
Science of The Total Environment.2022; 819: 152014. CrossRef
Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island
Geeta Chhetri, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
High-throughput absolute quantification sequencing reveals the effect of different fertilizer applications on bacterial community in a tomato cultivated coastal saline soil
Si-Qi Jiang, Ya-Nan Yu, Ren-Wei Gao, Huan Wang, Jian Zhang, Rong Li, Xiao-Hua Long, Qi-Rong Shen, Wei Chen, Feng Cai
Science of The Total Environment.2019; 687: 601. CrossRef
Pontibacter chitinilyticus sp. nov., a novel chitin-hydrolysing bacterium isolated from soil
Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Myung Kyum Kim, Taegun Seo
Antonie van Leeuwenhoek.2019; 112(7): 1011. CrossRef
Pontibacter locisalis Sy30T sp. nov. isolated from soil collected from an abandoned saltern
Yan-Xia Zhou, Zhi-Hong Xie, Jin-Xin Zhao, Zong-Jun Du, Guan-Jun Chen
Antonie van Leeuwenhoek.2016; 109(3): 415. CrossRef
Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field
Yue-Hong Wu, Peng Zhou, Shu-Ling Jian, Zhen-Sheng Liu, Chun-Sheng Wang, Aharon Oren, Xue-Wei Xu
International Journal of Systematic and Evolutionary Microbiology.2016; 66(4): 1760. CrossRef
Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake
Ghenijan Osman, Tao Zhang, Kai Lou, Yan Gao, Wei Chang, Qing Lin, Hong-Mei Yang, Xiang-Dong Huo, Ning Wang
International Journal of Systematic and Evolutionary Microbiology .2016; 66(12): 5523. CrossRef
Pontibacter mucosus sp. nov., isolated from hexachlorocyclohexane-contaminated pond sediment
Namita Nayyar, Puneet Kohli, Nitish Kumar Mahato, Rup Lal
International Journal of Systematic and Evolutionary Microbiology.2016; 66(6): 2234. CrossRef
Pontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil
N. K. Mahato, C. Tripathi, N. Nayyar, A. K. Singh, R. Lal
International Journal of Systematic and Evolutionary Microbiology.2016; 66(2): 1080. CrossRef
Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste
Amit Kumar Singh, Nidhi Garg, Rup Lal
International Journal of Systematic and Evolutionary Microbiology .2015; 65(Pt_7): 2248. CrossRef
Pontibacter humi sp. nov., Isolated from Mountain Soil
Sathiyaraj Srinivasan, Jae-Jin Lee, Sang-Seob Lee, Myung Kyum Kim
Current Microbiology.2014; 69(3): 263. CrossRef
Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae
Linghua Xu, Xian-Chun Zeng, Yao Nie, Xuesong Luo, Enmin Zhou, Lingli Zhou, Yunfan Pan, Wenjun Li, Paul Jaak Janssen
PLoS ONE.2014; 9(3): e92294. CrossRef

First
Prev
Page of 3
Next
Last

Search