Skip Navigation
Skip to contents

Journal of Microbiology : Journal of Microbiology

OPEN ACCESS
SEARCH
Search
Advanced Search
mobile menu button

Search

Page Path
HOME > Search
159 "taxonomy"
Filter
Filter
Article category
Keywords
More +
Publication year
More +
Authors
More +
Funded articles
Full article
Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater
Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho
J. Microbiol. 2025;63(8):e2504017.   Published online August 13, 2025
DOI: https://doi.org/10.71150/jm.2504017
  • 1,296 View
  • 58 Download
AbstractAbstract PDFSupplementary Material

Two Gram-stain-negative, obligately aerobic, non-motile, short rod-shaped bacteria, designated IMCC43871T and IMCC45206T, were isolated from coastal surface seawater collected from the Yellow Sea and the South Sea of Korea, respectively. The two strains shared 99.2% 16S rRNA gene sequence similarity with each other and exhibited ≤ 98.4% similarity to three described Rubrivirga species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between IMCC43871T and IMCC45206T were 88.5% and 36.3%, respectively, confirming that they represent two distinct species. Their ANI (≤ 77.7%) and dDDH (≤ 21.4%) values relative to the type strains of the genus Rubrivirga further supported the recognition of strains IMCC43871T and IMCC45206T as two novel species within the genus. The complete genomes of IMCC43871T (4.17 Mb, 71.8% G + C content) and IMCC45206T (4.17 Mb, 72.8% G + C content) fall within the known genomic range of the genus. Cellular fatty acid, quinone, and polar lipid profiles were consistent with the chemotaxonomic features of the genus Rubrivirga, supporting their affiliation with the genus. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43871T and IMCC45206T are proposed as two novel species, Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., respectively. The type strains are IMCC43871T (= KCTC 102072T = NBRC 116463T) and IMCC45206T (= KCTC 92925T = NBRC 116172T = CCTCC AB 2023136T).
Journal Articles
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
J. Microbiol. 2024;62(12):1089-1097.   Published online December 2, 2024
DOI: https://doi.org/10.1007/s12275-024-00188-z
  • 471 View
  • 18 Download
  • 1 Web of Science
  • 1 Crossref
AbstractAbstract PDF
Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01(T) and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01(T) and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003(T) and Leuconostoc gasicomitatum LMG 18811(T) with sequence similarities of 98.74%. The complete whole-genome sequences of strains MS01(T) and MS02 measured 2.04-2.06 Mbp and harbored a 50.6 kb plasmid, with DNA G + C contents of 37.7% for both. Based on average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values, both strains were confirmed to belong to the same species but showed ≤ 85.9% ANI and ≤ 29.9% dDDH values to other Leuconostoc species, indicating that they represent a novel species. Metabolic pathway reconstruction revealed that both strains perform heterolactic acid fermentation, producing lactate, acetate, and ethanol. Chemotaxonomic analyses, including cellular fatty acids, polar lipids, and peptidoglycan amino acid, confirmed the inclusion of both strains within the genus Leuconostoc. Based on the phylogenetic, genomic, and phenotypic characterization, strains MS01(T) and MS02 were considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc aquikimchii sp. nov. is proposed with MS01(T) (= KACC 23748(T) = JCM 37028(T)) as the type strain.

Citations

Citations to this article as recorded by  
  • Validation List no. 224. 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
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
J. Microbiol. 2024;62(9):739-748.   Published online July 18, 2024
DOI: https://doi.org/10.1007/s12275-024-00158-5
  • 531 View
  • 9 Download
  • 5 Web of Science
  • 5 Crossref
AbstractAbstract PDF
Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200(T) and IMCC45268(T), were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200(T) and IMCC45268(T) shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71(T) (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200(T) and IMCC45268(T) were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C(16:1) ω6c and/or C(16:1) ω7c) and summed feature 8 (comprising C(18:1) ω6c and/or C(18:1) ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200(T) and IMCC45268(T) were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200(T) (= KCTC 8133(T) = NBRC 116295(T) = CCTCC AB 2023139(T)) and IMCC45268(T) (= KCTC 92921(T) = NBRC 116135(T)) as the type strains, respectively.

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
  • Phycobium rhodophyticola gen. nov., sp. nov. and Aliiphycobium algicola gen. nov., sp. nov., isolated from the phycosphere of marine red algae
    Jeong Min Kim, Woonhee Baek, Byeong Jun Choi, Hülya Bayburt, Jae Kyeong Lee, Sung Chul Lee, Che Ok Jeon
    Journal of Microbiology.2025; 63(6): e2503014.     CrossRef
  • Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 42
    Aharon Oren, Markus Göker
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
  • Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., isolated from Korean coastal surface seawater
    Jisoo Han, Yeonjung Lim, Mirae Kim, Jang-Cheon Cho
    Journal of Microbiology.2025; 63(8): e2504017.     CrossRef
  • Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
    Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
    Journal of Microbiology.2024; 62(12): 1089.     CrossRef
Review
Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target
Yurim Yoon, Saemee Song
J. Microbiol. 2024;62(4):261-275.   Published online May 31, 2024
DOI: https://doi.org/10.1007/s12275-024-00137-w
  • 318 View
  • 9 Download
  • 2 Web of Science
  • 3 Crossref
AbstractAbstract PDF
Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.

Citations

Citations to this article as recorded by  
  • Boosting the Antimicrobial Activity of Quaternary Ammonium Photosensitizers by Janus‐Type AIE Luminogens
    Dongyang Fan, Meng Li, Zipeng Shen, Ying Li, Jingjing Guo, Dong Wang, Ting Han, Ben Zhong Tang
    Aggregate.2025;[Epub]     CrossRef
  • Functional Versatility of Vibrio cholerae Outer Membrane Proteins
    Annabelle Mathieu-Denoncourt, Marylise Duperthuy
    Applied Microbiology.2025; 5(3): 64.     CrossRef
  • Integrated Omics-Based Discovery of Bioactive Halogenated Metabolites from the Deep-Sea Streptomyces sp. B188M101
    Emmanuel Tope Oluwabusola, Stephen A. Jackson, Cristina Brunati, Stefanie Gackstatter, Hannah Vedder, Marianna Iorio, Gargee Chawande, Lekha Menon Margassery, Giang-Son Nguyen, David J. Clarke, Rainer Ebel, Marcel Jaspars, Alan D. W. Dobson
    Marine Drugs.2025; 23(9): 362.     CrossRef
Journal Articles
Medium Chain Length Polyhydroxyalkanoate Production by Engineered Pseudomonas gessardii Using Acetate-formate as Carbon Sources
Woo Young Kim, Seung-Jin Kim, Hye-Rin Seo, Yoonyong Yang, Jong Seok Lee, Moonsuk Hur, Byoung-Hee Lee, Jong-Geol Kim, Min-Kyu Oh
J. Microbiol. 2024;62(7):569-579.   Published online May 3, 2024
DOI: https://doi.org/10.1007/s12275-024-00136-x
  • 388 View
  • 7 Download
  • 4 Web of Science
  • 4 Crossref
AbstractAbstract PDF
Production of medium chain length polyhydroxyalkanoate (mcl-PHA) was attempted using Pseudomonas gessardii NIBRBAC000509957, which was isolated from Sunchang, Jeollabuk-do, Republic of Korea (35°24'27.7"N, 127°09'13.0"E) and effectively utilized acetate and formate as carbon sources. We first evaluated the utilization of acetate as a carbon source, revealing optimal growth at 5 g/L acetate. Then, formate was supplied to the acetate minimal medium as a carbon source to enhance cell growth. After overexpressing the acetate and formate assimilation pathway enzymes, this strain grew at a significantly higher rate in the medium. As this strain naturally produces PHA, it was further engineered metabolically to enhance mcl-PHA production. The engineered strain produced 0.40 g/L of mcl-PHA with a biomass content of 30.43% in fed-batch fermentation. Overall, this strain can be further developed to convert acetate and formate into valuable products.

Citations

Citations to this article as recorded by  
  • Formate-driven photoautotrophic growth and biopolymer storage in anaerobic purple bacteria
    Mohammad Adib Ghazali Abdul Rahman, Bronwyn Laycock, Steven Pratt, Damien J. Batstone
    Bioresource Technology.2025; 434: 132753.     CrossRef
  • Sulphide and oleic acid synergism in accelerating mcl-PHA biopolymer production in Pseudomonas aeruginosa MCC 5300 by modulating electron transport system
    Raghavendra Paduvari, Divyashree Somashekara
    Biochemistry and Biophysics Reports.2025; 44: 102286.     CrossRef
  • Unlocking efficient polyhydroxyalkanoate production by Gram-positive Priestia megaterium using waste-derived feedstocks
    Xinyi Bai, Libo Xu, Kang Li, Guangbao Zhang, Mengjun Zhang, Yi Huang
    Microbial Cell Factories.2025;[Epub]     CrossRef
  • Selective utilization of formic acid and acetic acid in succinic acid fermentation broth to produce single-cell protein using Rhodotorula glutinis
    Fuqiang Liu, Pengfei Wu, Lin Yu, Zitu Lü, Xinying Sun, Jiaxin Li, Lei Liu, Jing Wu, Jianan Zhang
    Bioprocess and Biosystems Engineering.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
J. Microbiol. 2024;62(4):277-284.   Published online March 6, 2024
DOI: https://doi.org/10.1007/s12275-024-00108-1
  • 355 View
  • 12 Download
AbstractAbstract PDF
We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038(T), from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C(15:0) and iso-C(17:0). Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038(T) has the highest similarity with Spelaeicoccus albus DSM 26341( T) (96.02%). ZFBP1038(T) formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038(T) was 63.65 mol% and the genome size was 4.05 Mb. Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038(T) and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively. Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038(T) represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038(T) (= EE 014( T) = GDMCC 1.3024( T) = JCM 35335( T)).
miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13
Wei Zeng , Jia Pan , Guannan Ye
J. Microbiol. 2024;62(2):63-73.   Published online February 24, 2024
DOI: https://doi.org/10.1007/s12275-023-00100-1
  • 406 View
  • 8 Download
  • 9 Web of Science
  • 9 Crossref
AbstractAbstract PDF
Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

Citations

Citations to this article as recorded by  
  • miR-135b: A key role in cancer biology and therapeutic targets
    Yingchun Shao, Shuangshuang Zhang, Yuxin Pan, Zhan Peng, Yinying Dong
    Non-coding RNA Research.2025; 12: 67.     CrossRef
  • miR‐135b: A Potential Biomarker for Pathological Diagnosis and Biological Therapy
    Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma
    WIREs RNA.2025;[Epub]     CrossRef
  • Effects of the Intestinal Microbiome and Metabolites on Neoadjuvant Chemotherapy Efficacy in Breast Cancer
    Jingyue Fu, Hongxin Lin, Shuaikang Li, Xingying Yu, Yufan Jin, Jie Mei, Yichao Zhu, Tiansong Xia
    BIO Integration.2025;[Epub]     CrossRef
  • Fusobacterium nucleatum and non-coding RNAs: orchestrating oncogenic pathways in colorectal cancer
    Zahra Sadeghloo, Sara Ebrahimi, Mojdeh Hakemi-Vala, Mehdi Totonchi, Amir Sadeghi, Nayeralsadat Fatemi
    Gut Pathogens.2025;[Epub]     CrossRef
  • Regulatory mechanisms and emerging diagnostic and therapeutic opportunities of non-coding RNAs in tumorigenesis: a pan-cancer perspective
    Doblin Sandai, Zengkan Du, Haoling Zhang, Qi Sun
    Critical Reviews in Clinical Laboratory Sciences.2025; : 1.     CrossRef
  • Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies
    Zhuangzhuang Shi, Zhaoming Li, Mingzhi Zhang
    Journal of Translational Medicine.2024;[Epub]     CrossRef
  • Fusobacterium nucleatum: a novel regulator of antitumor immune checkpoint blockade therapy in colorectal cancer
    Mengjie Luo
    American Journal of Cancer Research.2024; 14(8): 3962.     CrossRef
  • Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer
    Sevag Hamamah, Andrei Lobiuc, Mihai Covasa
    International Journal of Molecular Sciences.2024; 25(16): 9026.     CrossRef
  • Identification of Penexanthone A as a Novel Chemosensitizer to Induce Ferroptosis by Targeting Nrf2 in Human Colorectal Cancer Cells
    Genshi Zhao, Yanying Liu, Xia Wei, Chunxia Yang, Junfei Lu, Shihuan Yan, Xiaolin Ma, Xue Cheng, Zhengliang You, Yue Ding, Hongwei Guo, Zhiheng Su, Shangping Xing, Dan Zhu
    Marine Drugs.2024; 22(8): 357.     CrossRef
Structural and Functional Analyses of the Flavoprotein Disulfide Reductase FN0820 of Fusobacterium nucleatum
Hyunwoo Shin , Yeongjin Baek , Dukwon Lee , Yongbin Xu , Yonghoon Kwon , Inseong Jo , Nam-Chul Ha
J. Microbiol. 2023;61(12):1033-1041.   Published online December 20, 2023
DOI: https://doi.org/10.1007/s12275-023-00095-9
  • 379 View
  • 0 Download
  • 1 Web of Science
  • 1 Crossref
AbstractAbstract PDF
Escherichia coli RclA and Staphylococcus aureus MerA are part of the Group I flavoprotein disulfide reductase (FDR) family and have been implicated in the contribution to bacterial pathogenesis by defending against the host immune response. Fusobacterium nucleatum is a pathogenic, anaerobic Gram-negative bacterial species commonly found in the human oral cavity and gastrointestinal tract. In this study, we discovered that the F. nucleatum protein FN0820, belonging to the Group I FDR family, exhibited a higher activity of a Cu2+- dependent NADH oxidase than E. coli RclA. Moreover, FN0820 decreased the dissolved oxygen level in the solution with higher NADH oxidase activity. We found that L-tryptophan and its analog 5-hydroxytryptophan inhibit the FN0820 activities of NADH oxidase and the concomitant reduction of oxygen. Our results have implications for developing new treatment strategies against pathogens that defend the host immune response with Group I FDRs.

Citations

Citations to this article as recorded by  
  • The role of metals in hypothiocyanite resistance in Escherichia coli
    Michael J. Gray, Laurie E. Comstock
    Journal of Bacteriology.2024;[Epub]     CrossRef
Comparison of Ganoderma boninense Isolate’s Aggressiveness Using Infected Oil Palm Seedlings
Mei Lieng Lo , Tu Anh Vu Thanh , Frazer Midot , Sharon Yu Ling Lau , Wei Chee Wong , Hun Jiat Tung , Mui Sie Jee , Mei-Yee Chin , Lulie Melling
J. Microbiol. 2023;61(4):449-459.   Published online April 25, 2023
DOI: https://doi.org/10.1007/s12275-023-00040-w
  • 434 View
  • 0 Download
  • 6 Web of Science
  • 7 Crossref
AbstractAbstract PDF
Basal stem rot incidence caused by a white-rot fungus, Ganoderma boninense, is the major disease of oil palm in Southeast Asia. The rate of disease transmission and host damage are affected by variations in pathogen aggressiveness. Several other studies have used the disease severity index (DSI) to determine G. boninense aggressiveness levels while verifying disease using a culture-based method, which might not provide accurate results or be feasible in all cases. To differentiate G. boninense aggressiveness, we employed the DSI and vegetative growth measurement of infected oil palm seedlings. Disease confirmation was performed through scanning electron microscopy and molecular identification of fungal DNA from both infected tissue and fungi isolated from Ganoderma selective medium. Two-month-old oil palm seedlings were artificially inoculated with G. boninense isolates (2, 4A, 5A, 5B, and 7A) sampled from Miri (Lambir) and Mukah (Sungai Meris and Sungai Liuk), Sarawak. The isolates were categorized into three groups: highly aggressive (4A and 5B), moderately aggressive (5A and 7A), and less aggressive (2). Isolate 5B was identified as the most aggressive, and it was the only one to result in seedling mortality. Out of the five vegetative growth parameters measured, only the bole size between treatments was not affected. The integration of both conventional and molecular approaches in disease confirmation allows for precise detection.

Citations

Citations to this article as recorded by  
  • First Report of Ganoderma ryvardenii causing Basal Stem Rot (BSR) disease on oil palm (Elaeis guineensis Jacq.) in Ghana
    Emmanuellah Lekete-Lawson, Grace C. van der Puije, Enoch A. Osekre, Frank K. Ackah
    F1000Research.2025; 14: 413.     CrossRef
  • Gene expression of transcripts encoding putative secreted proteins from an oil palm fungal pathogen Ganoderma boninense
    Mui Sie Jee, Chai-Ling Ho, Mohd Termizi Yusof, Sharon Yu Ling Lau, Frazer Midot, Mei Lieng Lo, Mei-Yee Chin, Lulie Melling
    Physiological and Molecular Plant Pathology.2025; 138: 102715.     CrossRef
  • First Report of Ganoderma ryvardenii causing Basal Stem Rot (BSR) disease on oil palm (Elaeis guineensis Jacq.) in Ghana
    Emmanuellah Lekete-Lawson, Grace C. van der Puije, Enoch A. Osekre, Frank K. Ackah
    F1000Research.2025; 14: 413.     CrossRef
  • A review update on Ganoderma species: etiology and management approaches
    Pratibha Thakur, Sonali Khanal, Ashwani Tapwal, Neha Sharma, Poonam Chauhan, Tamanna Singh Thakur, Dinesh Kumar, Rachna Verma
    Antonie van Leeuwenhoek.2025;[Epub]     CrossRef
  • An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management
    Samantha C. Karunarathna, Nimesha M. Patabendige, Wenhua Lu, Suhail Asad, Kalani K. Hapuarachchi
    Journal of Fungi.2024; 10(6): 414.     CrossRef
  • Advancements in the nanodelivery of azole-based fungicides to control oil palm pathogenic fungi
    Azren Aida Asmawi, Fatmawati Adam, Nurul Aini Mohd Azman, Mohd Basyaruddin Abdul Rahman
    Heliyon.2024; 10(18): e37132.     CrossRef
  • Characterizations of Ganoderma species causing basal stem rot disease in coconut tree
    Umesh Sajjan, Manjunath Hubballi, Abhay K. Pandey, V. Devappa, H. P. Maheswarappa
    3 Biotech.2024;[Epub]     CrossRef
Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
Kang Xiao , Zhengyu Chen , Qin Long
J. Microbiol. 2023;61(5):571-578.   Published online April 21, 2023
DOI: https://doi.org/10.1007/s12275-023-00045-5
  • 368 View
  • 0 Download
  • 3 Web of Science
  • 2 Crossref
AbstractAbstract PDF
Microbial communities played a vital role in maintaining homeostasis of ocular surface. However, no studies explored the myopia-associated conjunctiva microbiota changes until now. In this study, conjunctival sac swab specimens were collected from 12 eyes of low myopia (LM), and 14 eyes of high myopia (HM) patients. The V3–V4 region of the 16S rRNA gene was amplified and then sequenced. Statistical analysis was performed to investigate differences in the taxonomy and diversity between two groups. Compared to LM, higher Ocular Surface Disease Index (OSDI) scores were observed in HM group. The Shannon index of the HM was lower than that of the LM group (P = 0.017). Principle coordinate analysis and Partial Least Squares Discrimination Analysis showed distinct microbiome composition between two groups. At the phylum level, there were higher relative abundances of Proteobacteria (68.27% vs 38.51%) and lower abundances of Actinobacteria (3.71% vs 9.19%) in HM, compared to LM group (P = 0.031, 0.010, respectively). At the genus level, the abundances of Acinetobacter in HM (18.16%) were significantly higher than the LM (6.52%) group (P = 0.011). Actinobacteria levels were negatively correlated with the myopic spherical equivalent and OSDI scores. Moreover, positive correlations were found between Proteobacteria levels and OSDI scores, Acinetobacter levels were positively correlated with myopic spherical equivalent and OSDI scores. In conclusion, HM Patients have bacterial microbiota imbalance in the conjunctival sac, compared with LM patients. Proteobacteria, Actinobacteria, Acinetobacter may play roles in the HM associated ocular surface irritation.

Citations

Citations to this article as recorded by  
  • Harnessing Lactiplantibacillus plantarum EP21 and its membrane vesicles to inhibit myopia development
    Chi-Fong Lin, Yu-An Hsu, Yung-Lan Chou, Ying-Chi Chen, En-Shyh Lin, Peng-Tai Tien, Jamie jiin-Yi Chen, Ming-Yen Wu, Chia-Hung Lin, Hui-Ju Lin, Lei Wan
    Gut Microbes.2025;[Epub]     CrossRef
  • Gut Microbiota Profiles in Myopes and Nonmyopes
    Wan E. W. Omar, Gurdeep Singh, Andrew J. McBain, Fiona Cruickshank, Hema Radhakrishnan
    Investigative Ophthalmology & Visual Science.2024; 65(5): 2.     CrossRef
CXCL12/CXCR4 Axis is Involved in the Recruitment of NK Cells by HMGB1 Contributing to Persistent Airway Inflammation and AHR During the Late Stage of RSV Infection
Sisi Chen , Wei Tang , Guangyuan Yu , Zhengzhen Tang , Enmei Liu
J. Microbiol. 2023;61(4):461-469.   Published online February 13, 2023
DOI: https://doi.org/10.1007/s12275-023-00018-8
  • 362 View
  • 0 Download
  • 9 Web of Science
  • 9 Crossref
AbstractAbstract PDF
We previously showed that both high-mobility group box-1 (HMGB1) and natural killer (NK) cells contribute to respiratory syncytial virus (RSV)-induced persistent airway inflammation and airway hyperresponsiveness (AHR). Meanwhile, Chemokine (C-X-C motif) ligand 12 (CXCL12) and its specific receptor (chemokine receptor 4, CXCR4) play important roles in recruitment of immune cells. CXCL12 has been reported to form a complex with HMGB1 that binds to CXCR4 and increases inflammatory cell migration. The relationship between HMGB1, NK cells and chemokines in RSV-infected model remains unclear. An anti-HMGB1 neutralizing antibody and inhibitor of CXCR4 (AMD3100) was administered to observe changes of NK cells and airway disorders in nude mice and BALB/c mice. Results showed that the mRNA expression and protein levels of HMGB1 were elevated in late stage of RSV infection and persistent airway inflammation and AHR were diminished after administration of anti-HMGB1 antibodies, with an associated significant decrease in CXCR4+ NK cells. In addition, CXCL12 and CXCR4 were reduced after HMGB1 blockade. Treatment with AMD3100 significantly suppressed the recruitment of NK cells and alleviated the airway disorders. Thus, CXCL12/CXCR4 axis is involved in the recruitment of NK cells by HMGB1, contributing to persistent airway inflammation and AHR during the late stage of RSV infection.

Citations

Citations to this article as recorded by  
  • Exploring Ribosomal Genes as Potential Biomarkers of the Immune Microenvironment in Respiratory Syncytial Virus Infection
    Lu Lin, Zenghua Liao, Chaoqian Li
    Biochemical Genetics.2025; 63(2): 1839.     CrossRef
  • Damage-associated molecular patterns in viral infection: potential therapeutic targets
    Huizhen Tian, Qiong Liu, Xiaomin Yu, Yanli Cao, Xiaotian Huang
    Critical Reviews in Microbiology.2025; 51(3): 514.     CrossRef
  • Peptides targeting RAB11A–FIP2 complex inhibit HPIV3, RSV, and IAV replication as broad-spectrum antivirals
    Yanliang Jiang, Yongliang Zhao, Jie Deng, Xiaoyan Wu, Jian Li, Dong Guo, Ke Xu, Yali Qin, Mingzhou Chen
    Cell & Bioscience.2025;[Epub]     CrossRef
  • Inhibition of the TLR4/RAGE pathway by clearance of extracellular HMGB1 is a potential therapeutic target for radiation-damaged salivary glands
    Takashi I, Riho Kanai, Makoto Seki, Hideki Agata, Hideaki Kagami, Hiroshi Murata, Izumi Asahina, Simon D. Tran, Yoshinori Sumita
    Regenerative Therapy.2025; 30: 476.     CrossRef
  • Respiratory Syncytial Virus (RSV): A Comprehensive Overview From Basic Biology to Clinical Prevention and Control
    Jie Shi, Xiya Huang, Chunjun Ye, Yishan Lu, Yanyan Liu, Yuquan Wei, Xiawei Wei
    Medicinal Research Reviews.2025;[Epub]     CrossRef
  • DAMPs in immunosenescence and cancer
    Fangquan Chen, Hu Tang, Xiutao Cai, Junhao Lin, Rui Kang, Daolin Tang, Jiao Liu
    Seminars in Cancer Biology.2024; 106-107: 123.     CrossRef
  • Advancements in Stimulus-Responsive Co-Delivery Nanocarriers for Enhanced Cancer Immunotherapy
    Meng-Ru Zhang, Lin-Lin Fang, Yang Guo, Qin Wang, You-Jie Li, Hong-Fang Sun, Shu-Yang Xie, Yan Liang
    International Journal of Nanomedicine.2024; Volume 19: 3387.     CrossRef
  • Immunomodulatory markers and therapies for the management of infant respiratory syncytial virus infection
    Ricardo A. Loaiza, Mónica A. Farías, Catalina A. Andrade, Mario A. Ramírez, Linmar Rodriguez-Guilarte, José T. Muñóz, Pablo A. González, Susan M. Bueno, Alexis M. Kalergis
    Expert Review of Anti-infective Therapy.2024; 22(8): 631.     CrossRef
  • Activin A, a Novel Chemokine, Induces Mouse NK Cell Migration via AKT and Calcium Signaling
    Yunfeng Wang, Zhonghui Liu, Yan Qi, Jiandong Wu, Boyang Liu, Xueling Cui
    Cells.2024; 13(9): 728.     CrossRef
Review
Recent Advances in CRISPR‑Cas Technologies for Synthetic Biology
Song Hee Jeong , Ho Joung Lee , Sang Jun Lee
J. Microbiol. 2023;61(1):13-36.   Published online February 1, 2023
DOI: https://doi.org/10.1007/s12275-022-00005-5
  • 1,788 View
  • 0 Download
  • 34 Web of Science
  • 36 Crossref
AbstractAbstract PDF
With developments in synthetic biology, “engineering biology” has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.

Citations

Citations to this article as recorded by  
  • Sustainable Approaches for Managing Phthalate Pollution: Navigating Challenges, and Establishing the Future of Environmental Protection
    Eswar Marcharla, Smarika Chauhan, Sneha Hariharan, Parthipan Punniyakotti, Thanigaivel Sundaram, Swamynathan Ganesan, Woong Kim, Muthusamy Govarthanan
    Advanced Sustainable Systems.2025;[Epub]     CrossRef
  • CRISPR applications in microbial World: Assessing the opportunities and challenges
    Farhan Kursheed, Esha Naz, Sana Mateen, Ume Kulsoom
    Gene.2025; 935: 149075.     CrossRef
  • From Spores to Suffering: Understanding the Role of Anthrax in Bioterrorism
    Ratnesh Singh Kanwar, Kirtida Gambhir, Tanishka Aggarwal, Akash Godiwal, Kuntal Bhadra
    Military Medicine.2025; 190(3-4): e569.     CrossRef
  • Unveiling the potential of gene editing techniques in revolutionizing Cancer treatment: A comprehensive overview
    Pankaj Garg, Gargi Singhal, Siddhika Pareek, Prakash Kulkarni, David Horne, Aritro Nath, Ravi Salgia, Sharad S. Singhal
    Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(1): 189233.     CrossRef
  • From nanotechnology to AI: The next generation of CRISPR-based smart biosensors for infectious disease detection
    Irkham, Abdullahi Umar Ibrahim, Chidi Wilson Nwekwo, Pwadubashiyi Coston Pwavodi, Salma Nur Zakiyyah, Mehmet Ozsoz, Yeni Wahyuni Hartati
    Microchemical Journal.2025; 208: 112577.     CrossRef
  • Prospects for synthetic biology in 21st century agriculture
    Xingyan Ye, Kezhen Qin, Alisdair R. Fernie, Youjun Zhang
    Journal of Genetics and Genomics.2025; 52(8): 967.     CrossRef
  • Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy
    Mohd Afaque Ansari, Damini Verma, Mohd-Akmal Hamizan, Maumita Das Mukherjee, Noor Faizah Mohd-Naim, Minhaz Uddin Ahmed
    ACS Synthetic Biology.2025; 14(1): 21.     CrossRef
  • Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations
    Mehran khan, Mir Muhammad Nizamani, Muhammad Asif, Ali Kamran, Guandi He, Xiangyang Li, Sanwei Yang, Xin Xie
    Journal of Environmental Management.2025; 374: 123969.     CrossRef
  • Cell-free systems: A synthetic biology tool for rapid prototyping in metabolic engineering
    Kumyoung Jeung, Minsun Kim, Eunsoo Jang, Yang Jun Shon, Gyoo Yeol Jung
    Biotechnology Advances.2025; 79: 108522.     CrossRef
  • Synthetic biology and parasite genomics: engineering parasite-resistant human microbiomes for sustainable disease prevention
    Esam S. Al-Malki
    Beni-Suef University Journal of Basic and Applied Sciences.2025;[Epub]     CrossRef
  • Engineering Useful Microbial Species for Pharmaceutical Applications
    Amankeldi K. Sadanov, Baiken B. Baimakhanova, Saltanat E. Orasymbet, Irina A. Ratnikova, Zere Z. Turlybaeva, Gul B. Baimakhanova, Aigul A. Amitova, Anel A. Omirbekova, Gulzat S. Aitkaliyeva, Bekzhan D. Kossalbayev, Ayaz M. Belkozhayev
    Microorganisms.2025; 13(3): 599.     CrossRef
  • Engineering biology applications for environmental solutions: potential and challenges
    David J. Lea-Smith, Francis Hassard, Frederic Coulon, Natalie Partridge, Louise Horsfall, Kyle D. J. Parker, Robert D. J. Smith, Ronan R. McCarthy, Boyd McKew, Tony Gutierrez, Vinod Kumar, Gabriella Dotro, Zhugen Yang, Thomas P. Curtis, Peter Golyshin, So
    Nature Communications.2025;[Epub]     CrossRef
  • PlastiCRISPR: Genome Editing-Based Plastic Waste Management with Implications in Polyethylene Terephthalate (PET) Degradation
    Puja Palit, Maya Minkara, Maisha Abida, Safa Marwa, Chandrima Sen, Ayan Roy, Md Ridoan Pasha, Paulraj Selvakumar Mosae, Ayan Saha, Jannatul Ferdoush
    Biomolecules.2025; 15(5): 684.     CrossRef
  • Bioelectrocatalysis for solar fuels and sustainable energy
    Rodrigo M. Iost, Senentxu Lanceros-Méndez, Frank N. Crespilho
    Catalysis Science & Technology.2025; 15(13): 3793.     CrossRef
  • Shaping the Plant Specialized Metabolites Through Modern Breeding Technique
    Sayanti Mandal
    Molecular Biotechnology.2025;[Epub]     CrossRef
  • Probiotics in integrative medicine: Bridging the gap between traditional and modern approaches
    Sowndharya Bhavani, Marimuthu Chinnakannu, Saravanan Anbalagan, Sundaram Agaram, Shivani Chopra
    Scripta Medica.2025; 56(3): 537.     CrossRef
  • The dual promise of oncolytic viruses: selective targeting and therapeutic enhancement in cancer treatment
    Alaa A. A. Aljabali, Rasha Bashatwah, Omar Gammoh
    Exploration of Immunology.2025;[Epub]     CrossRef
  • Controlling CRISPR-Cas9 genome editing in human cells using a molecular glue degrader
    Namita Khajanchi, Vrusha Patel, Ronak Dua, Meha Kabra, Bikash R. Pattnaik, Krishanu Saha
    Molecular Therapy Nucleic Acids.2025; 36(3): 102640.     CrossRef
  • Multigene engineering in plants: Technologies, applications, and future prospects
    Ruchika Rajput, Brandon A. Boone, Rushil Mandlik, Md Torikul Islam, Yiping Qi, Jack Wang, Rodolphe Barrangou, Rosangela Sozzani, Carrie A. Eckert, Gerald A. Tuskan, Jin-Gui Chen, Xiaohan Yang
    Biotechnology Advances.2025; 85: 108697.     CrossRef
  • Bacterial peptide antibiotics: A comprehensive review on biosynthesis, mechanisms, and therapeutic potential
    Nagarjuna Prakash Dalbanjan, Karuna Korgaonkar, Rajesh Parvatkar, Supriya Tilvi, Praveen Kumar S．K．
    Next Research.2025; 2(4): 100850.     CrossRef
  • Isolation, identification, culture, extraction of natural compounds from microbes derived from fruit and vegetable wastes, and biological activity screening: A systematic review and meta-analysis
    Shreyasi Ray, Aishik Banerjee, Debasmita Paul, Soumyadeep Paul, Biplab Debnath, Shaileyee Das
    Next Research.2025; 2(3): 100627.     CrossRef
  • Systems biology for mushroom cultivation promoting quality life
    Shilpa Malakar, Priya Sutaoney, Priyambada Singh, Kamal Shah, Nagendra Singh Chauhan
    Circular Agricultural Systems.2025;[Epub]     CrossRef
  • Biotechnological innovations for microplastic degradation: A synthetic biology perspective
    Pooja Yadav, Chitra Yadav, Abhishek Joshi, Mukesh Meena, Jaya Arora
    Next Research.2025; 2(4): 100878.     CrossRef
  • AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach
    Serena Rosignoli, Elisa Lustrino, Alessio Conci, Alessandra Fabrizi, Serena Rinaldo, Maria Carmela Latella, Elena Enzo, Gianni Prosseda, Laura De Rosa, Michele De Luca, Alessandro Paiardini
    Nucleic Acids Research.2024; 52(W1): W29.     CrossRef
  • Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing
    Song Hee Jeong, Ho Joung Lee, Sang Jun Lee
    Frontiers in Genome Editing.2024;[Epub]     CrossRef
  • Developing pioneering pharmacological strategies with CRISPR/Cas9 library screening to overcome cancer drug resistance
    Yu He, Huan Li, Xueming Ju, Bo Gong
    Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2024; 1879(6): 189212.     CrossRef
  • Efficient CRISPR-Cas12f1-Mediated Multiplex Bacterial Genome Editing via Low-Temperature Recovery
    Se Ra Lim, Hyun Ju Kim, Sang Jun Lee
    Journal of Microbiology and Biotechnology.2024; 34(7): 1522.     CrossRef
  • CRISPR-based biosensor for the detection of Marburg and Ebola virus
    Irkham Irkham, Abdullahi Umar Ibrahim, Pwadubashiyi Coston Pwavodi, Chidi Wilson Nwekwo, Yeni Wahyuni Hartati
    Sensing and Bio-Sensing Research.2024; 43: 100601.     CrossRef
  • Advancements in Synthetic Biology for Enhancing Cyanobacterial Capabilities in Sustainable Plastic Production: A Green Horizon Perspective
    Taufiq Nawaz, Liping Gu, Zhong Hu, Shah Fahad, Shah Saud, Ruanbao Zhou
    Fuels.2024; 5(3): 394.     CrossRef
  • Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking Advantage of CRISPR
    Piao Yang, Abraham Condrich, Ling Lu, Sean Scranton, Camina Hebner, Mohsen Sheykhhasan, Muhammad Azam Ali
    DNA.2024; 4(4): 427.     CrossRef
  • Perspective Evaluation of Synthetic Biology Approaches for Effective Mitigation of Heavy Metal Pollution
    Sandhya Mishra, Anju Patel, Pankaj Bhatt, Shaohua Chen, Pankaj Kumar Srivastava
    Reviews of Environmental Contamination and Toxicology.2024;[Epub]     CrossRef
  • Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine
    Asiya Nazir, Fathima Hasnain Nadeem Hussain, Afsheen Raza
    Frontiers in Bioengineering and Biotechnology.2024;[Epub]     CrossRef
  • Multifaceted Applications of Synthetic Microbial Communities: Advances in Biomedicine, Bioremediation, and Industry
    Edgar Adrian Contreras-Salgado, Ana Georgina Sánchez-Morán, Sergio Yair Rodríguez-Preciado, Sonia Sifuentes-Franco, Rogelio Rodríguez-Rodríguez, José Macías-Barragán, Mariana Díaz-Zaragoza
    Microbiology Research.2024; 15(3): 1709.     CrossRef
  • Biotechnological production of omega-3 fatty acids: current status and future perspectives
    Jiansong Qin, Elif Kurt, Tyler LBassi, Lucas Sa, Dongming Xie
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Emerging Technologies in Industrial Microbiology: From Bioengineering to CRISPR-Cas Systems
    Umar Farooq, Malathi Hanumanthayya, Izharul Haq
    Salud, Ciencia y Tecnología.2023; 3: 406.     CrossRef
  • Optimized Linear DNA Recombineering for CRISPR-Cpf1 System in Corynebacterium glutamicum
    Ting Wang, Xiaowan Jiang, Shufang Lv, Linfeng Hu, Shuangcheng Gao, Qingyang Xu, Junhui Zhang, Dianyun Hou
    Fermentation.2023; 10(1): 31.     CrossRef
Journal Articles
Description of Deefgea piscis sp. nov., and Deefgea tanakiae sp. nov., isolated from the gut of Korean indigenous fish
Do-Hun Gim , So-Yeon Lee , Jeong Eun Han , Jae-Yun Lee , Seo Min Kang , Jin-Woo Bae
J. Microbiol. 2022;60(11):1061-1069.   Published online September 1, 2022
DOI: https://doi.org/10.1007/s12275-022-2250-5
  • 388 View
  • 0 Download
  • 6 Web of Science
  • 7 Crossref
AbstractAbstract PDF
Three novel strains, (D17T, D13, and D25T) isolated from the gut of the Korean dark sleeper (Odontobutis platycephala), Kumgang fat minnow (Rhynchocypris kumgangensis), and the Korean oily bitterling (Tanakia koreensis) were identified as two novel species. Strains D17T and D13 showed the highest similarities in 16S rRNA gene and complete genome sequences to Deefgea rivuli WB 3.4-79T (98.0% and 97.9%, respectively, of 16S rRNA gene sequence similarity, 77.8% and 77.7%, respectively, of orthologous average nucleotide identity, Ortho- ANI, and 21.9% and 21.9%, respectively, of digital DNA-DNA hybridization, dDDH). Strain D17T showed the highest similarities in 16S rRNA gene and complete genome sequences to D13 (99.9% of 16S rRNA gene sequence similarity, 91.8% of OrthoANI, and 45.1% of dDDH); therefore, strains D17T and D13 were assigned as the same species. Strain D25T showed the highest similarities in 16S rRNA gene and complete genome sequences to D. chitinilytica Nsw-4T (98.2% of 16S rRNA gene sequence similarity, 82.4% of OrthoANI, and 25.1% of dDDH). Strains D17T and D13 were Gram-stain-negative, facultative anaerobes, rod-shaped, non-motile, and non-flagellated. Strain D25T was Gram-stain-negative, facultative anaerobe, rodshaped, and motile by a single polar flagellum. These strains had C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as the major cellular fatty acids and possessed Q-8 as a major respiratory ubiquinone. All three strains contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. Based on polyphasic taxonomic data, strains D17T, D13, and D25T represent two novel species of the genus Deefgea. We propose the name Deefgea piscis sp. nov. for strains D17T (= KCTC 82958T = JCM 34941T) and D13 (= KCTC 92368), and Deefgea tanakiae sp. nov. for strain D25T (= KCTC 82959T = JCM 34942T).

Citations

Citations to this article as recorded by  
  • Systematic Literature Review Identifying Core Genera in the Gut Microbiome of Rainbow Trout (Oncorhynchus mykiss) and Species‐level Microbial Community Analysis Using Long‐Read Amplicon Sequencing
    Mio Takeuchi, Kazuhiro Sugahara
    Aquaculture, Fish and Fisheries.2025;[Epub]     CrossRef
  • Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations
    Javier Edo Varg, Jaelle C. Brealey, David Benhaïm, Rafael Losada-Germain, Janette W. Boughman
    npj Biofilms and Microbiomes.2025;[Epub]     CrossRef
  • Fecal metagenomic and metabolomic analyses reveal non-invasive biomarkers of Flavobacterium psychrophilum infection in ayu ( Plecoglossus altivelis )
    Mio Takeuchi, Erina Fujiwara-Nagata, Kyohei Kuroda, Kenji Sakata, Takashi Narihiro, Jun Kikuchi, Katherine McMahon
    mSphere.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
  • An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
    Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
    Journal of Clinical Microbiology.2024;[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
  • Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
    Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
    PLOS ONE.2023; 18(12): e0289072.     CrossRef
[Protocol] Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method
Jaemin Lee , Minkyung Ryu , Dayeong Bae , Hong-Man Kim , Seong-il Eyun , Jeehyeon Bae , Kangseok Lee
J. Microbiol. 2022;60(7):659-667.   Published online June 22, 2022
DOI: https://doi.org/10.1007/s12275-022-2235-4
  • 351 View
  • 0 Download
  • 6 Web of Science
  • 6 Crossref
AbstractAbstract PDF
Aptamers are short single-stranded DNA or RNA oligonucleotides capable of binding with high affinity and specificity to target molecules. Because of their durability and ease of synthesis, aptamers are used in a wide range of biomedical fields, including the diagnosis of diseases and targeted delivery of therapeutic agents. The aptamers were selected using a process called systematic evolution of ligands by exponential enrichment (SELEX), which has been improved for various research purposes since its development in 1990. In this protocol, we describe a modified SELEX method that rapidly produces high aptamer screening yields using two types of magnetic beads. Using this method, we isolated an aptamer that specifically binds to an antimicrobial peptide. We suggest that by conjugating a small therapeutic-specific aptamer to a gold nanoparticle-based delivery system, which enhances the stability and intracellular delivery of peptides, aptamers selected by our method can be used for the development of therapeutic agents utilizing small therapeutic peptides.

Citations

Citations to this article as recorded by  
  • Recent approaches in the application of antimicrobial peptides in food preservation
    Satparkash Singh, Bhavna Jha, Pratiksha Tiwari, Vinay G. Joshi, Adarsh Mishra, Yashpal Singh Malik
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • Design and application of microfluidics in aptamer SELEX and Aptasensors
    Shikun Zhang, Yingming Zhang, Zhiyuan Ning, Mengxia Duan, Xianfeng Lin, Nuo Duan, Zhouping Wang, Shijia Wu
    Biotechnology Advances.2024; 77: 108461.     CrossRef
  • Nanogenosensors based on aptamers and peptides for bioelectrochemical cancer detection: an overview of recent advances in emerging materials and technologies
    Babak Mikaeeli Kangarshahi, Seyed Morteza Naghib
    Discover Applied Sciences.2024;[Epub]     CrossRef
  • Recent progress of SELEX methods for screening nucleic acid aptamers
    Chao Zhu, Ziru Feng, Hongwei Qin, Lu Chen, Mengmeng Yan, Linsen Li, Feng Qu
    Talanta.2024; 266: 124998.     CrossRef
  • Aptamer-conjugated gold nanoparticles platform as the intracellular delivery of antibodies for cancer therapy
    Ji-Hyun Yeom, Eunkyoung Shin, Hanyong Jin, Haifeng Liu, Yongyang Luo, Youngwoo Nam, Minkyung Ryu, Wooseok Song, Heeyoun Chi, Jeongkyu Kim, Kangseok Lee, Jeehyeon Bae
    Journal of Industrial and Engineering Chemistry.2023; 126: 480.     CrossRef
  • Regulation of transforming growth factor-β signaling as a therapeutic approach to treating colorectal cancer
    Jana Maslankova, Ivana Vecurkovska, Miroslava Rabajdova, Jana Katuchova, Milos Kicka, Michala Gayova, Vladimir Katuch
    World Journal of Gastroenterology.2022; 28(33): 4744.     CrossRef
Comparative analysis of the colistin resistance-regulating gene cluster in Klebsiella species
Sun Ju Kim , Hongbaek Cho , Kwan Soo Ko
J. Microbiol. 2022;60(5):461-468.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1640-z
  • 367 View
  • 1 Download
  • 3 Web of Science
  • 3 Crossref
AbstractAbstract PDF
CrrAB two-component regulatory system is associated with colistin resistance in Klebsiella pneumoniae. Recently, some K. pneumoniae isolates lacking crrAB genes have been identified. In this study, we investigated the distribution and structural variation of the crrBAC-kexD cluster. To evaluate the structural variation of the crrBAC-kexD cluster, we explored 59 clinical K. pneumoniae isolates from Korea, and 508 whole genomes of K. pneumoniae and other strains of Klebsiella sp. Significant structural variations in crrBAC-kexD and its surrounding regions were identified among K. pneumoniae genomes. Within the genus Klebsiella, the cluster was identified only in K. pneumoniae, K. variicola, and K. quasipneumoniae, which form the K. pneumoniae complex. Among the 304 available K. pneumoniae genomes, an intact crrBAC-kexD cluster was identified in 178 isolates (58.6%), while the cluster was absent in 90 isolates (29.6%). Partial deletions within the cluster were identified in 22 genomes (7.2%). The most diverse structural patterns of the crrBAC-kexD cluster were observed in ST11 strains. Some clades lacked the crrBAC-kexD cluster. The crrBAC-kexD cluster was identified in the genomes of other bacterial species, including Citrobacter freundii and Enterobacter ludwigii. The crrBAC-kexD cluster is proposed to have been acquired by the ancestor of the K. pneumoniae complex from other bacterial species and the cluster may have been lost and re-acquired repeatedly in K. pneumoniae strains according to the phylogenetic analysis. The dynamic evolution of the crrBAC-kexD cluster suggests that it may have other roles, in addition to colistin resistance, in bacterial physiology.

Citations

Citations to this article as recorded by  
  • High prevalence of polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae and its within-host evolution to resistance among critically ill scenarios
    Xiaoli Wang, Tianjiao Meng, Yunqi Dai, Hong-Yu Ou, Meng Wang, Bin Tang, Jingyong Sun, Decui Cheng, Tingting Pan, Ruoming Tan, Hongping Qu
    Infection.2025; 53(1): 271.     CrossRef
  • Roles of crrAB two-component regulatory system in Klebsiella pneumoniae: growth yield, survival in initial colistin treatment stage, and virulence
    Sun Ju Kim, Jong Hyun Shin, Hyunkeun Kim, Kwan Soo Ko
    International Journal of Antimicrobial Agents.2024; 63(1): 107011.     CrossRef
  • Role of efflux pumps, their inhibitors, and regulators in colistin resistance
    Yinhuan Ding, Jingchen Hao, Weijia Xiao, Caihong Ye, Xue Xiao, Chunxia Jian, Min Tang, Guangrong Li, Jinbo Liu, Zhangrui Zeng
    Frontiers in Microbiology.2023;[Epub]     CrossRef
Integrated proteomic and metabolomic analyses reveal significant changes in chloroplasts and mitochondria of pepper (Capsicum annuum L.) during Sclerotium rolfsii infection
Hongdong Liao , Xiangyu Wen , Xuelei Deng , Yonghong Wu , Jianping Xu , Xin Li , Shudong Zhou , Xuefeng Li , Chunhui Zhu , Feng Luo , Yanqing Ma , Jingyuan Zheng
J. Microbiol. 2022;60(5):511-525.   Published online March 31, 2022
DOI: https://doi.org/10.1007/s12275-022-1603-4
  • 340 View
  • 0 Download
  • 8 Web of Science
  • 8 Crossref
AbstractAbstract PDF
Infection by Sclerotium rolfsii will cause serious disease and lead to significant economic losses in chili pepper. In this study, the response of pepper during S. rolfsii infection was explored by electron microscopy, physiological determination and integrated proteome and metabolome analyses. Our results showed that the stomata of pepper stems were important portals for S. rolfsii infection. The plant cell morphology was significantly changed at the time of the fungal hyphae just contacting (T1) or surrounding (T2) the pepper. The chlorophyll, carotenoid, and MDA contents and the activities of POD, SOD, and CAT were markedly upregulated at T1 and T2. Approximately 4129 proteins and 823 metabolites were clearly identified in proteome and metabolome analyses, respectively. A change in 396 proteins and 54 metabolites in pepper stem tissues was observed at T1 compared with 438 proteins and 53 metabolites at T2. The proteins and metabolites related to photosynthesis and antioxidant systems in chloroplasts and mitochondria were disproportionally affected by S. rolfsii infection, impacting carbohydrate and amino acid metabolism. This study provided new insights into the response mechanism in pepper stems during S. rolfsii infection, which can guide future work on fungal disease resistance breeding in pepper.

Citations

Citations to this article as recorded by  
  • Sensitivity determination and resistance mechanism of Sclerotium rolfsii to difenoconazole
    Chaofan Jiang, Lin Zhou, Mengke Wang, Sirui Shen, Weifeng Cheng, Qingchen Zhao, Kaidi Cui, Leiming He
    Pest Management Science.2025; 81(6): 2734.     CrossRef
  • The “Coexistence” of Ehrlich pathway and de novo pathway improves 2-PE synthesis in Saccharomyces cerevisiae
    Chenghan Yang, Qingqing Lv, Li Zhang, Huining Jia, Hailong Chen, Sainan Yang, Yuxin Qiu, Haifeng Hang, Ali Mohsin, Ju Chu, Yingping Zhuang, Xiwei Tian
    Chemical Engineering Journal.2025; 516: 163688.     CrossRef
  • Effects of fungicide application on susceptible pepper cultivar under southern blight stress
    Rong Wen, Dandan Song, Chuanjing Liang, Gratien Twagirayezu, Yongping Wang, Dehui Tu, Zhenyi Luo, Shicai Zhang, Dan Xing, Zhibing Wu, Kangyun Wu
    Scientia Horticulturae.2025; 342: 114030.     CrossRef
  • Multifaceted chemical and bioactive features of Ag@TiO2 and Ag@SeO2 core/shell nanoparticles biosynthesized using Beta vulgaris L. extract
    Khaled M. Elattar, Fatimah O. Al-Otibi, Mohammed S. El-Hersh, Attia A. Attia, Noha M. Eldadamony, Ashraf Elsayed, Farid Menaa, WesamEldin I.A. Saber
    Heliyon.2024; 10(7): e28359.     CrossRef
  • Fighting for Survival at the Stomatal Gate
    Maeli Melotto, Brianna Fochs, Zachariah Jaramillo, Olivier Rodrigues
    Annual Review of Plant Biology .2024; 75(1): 551.     CrossRef
  • Zinc and Boron Soil Applications Affect Athelia rolfsii Stress Response in Sugar Beet (Beta vulgaris L.) Plants
    Tamalika Bhadra, Chandan Kumar Mahapatra, Md. Hosenuzzaman, Dipali Rani Gupta, Abeer Hashem, Graciela Dolores Avila-Quezada, Elsayed Fathi Abd_Allah, Md. Anamul Hoque, Swapan Kumar Paul
    Plants.2023; 12(19): 3509.     CrossRef
  • Genetic Regulation, Environmental Cues, and Extraction Methods for Higher Yield of Secondary Metabolites in Capsicum
    Khushbu Islam, Abdul Rawoof, Ajay Kumar, John Momo, Ilyas Ahmed, Meenakshi Dubey, Nirala Ramchiary
    Journal of Agricultural and Food Chemistry.2023; 71(24): 9213.     CrossRef
  • Integrated pathological, proteomic and metabolomic analyses reveal significant changes of Eriocheir sinensis hepatopancreatic in response to the microsporidian Hepatospora eriocheir infection
    Libo Hou, Mengdi Wang, Hao Li, Lei Zhu, Xianghui Kong, Wei Gu, Keran Bi, Jie Du, Qingguo Meng
    Aquaculture.2023; 577: 739994.     CrossRef
Exploiting the antibacterial mechanism of phenazine substances from Lysobacter antibioticus 13-6 against Xanthomonas oryzae pv. oryzicola
Qi Liu , Jun Yang , Waqar Ahmed , Xiaoyan Wan , Lanfang Wei , Guanghai Ji
J. Microbiol. 2022;60(5):496-510.   Published online March 31, 2022
DOI: https://doi.org/10.1007/s12275-022-1542-0
  • 369 View
  • 0 Download
  • 21 Web of Science
  • 20 Crossref
AbstractAbstract PDF
Bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most destructive diseases affecting rice production worldwide. In this study, we extracted and purified phenazine substances from the secondary metabolites of Lysobacter antibioticus 13-6. The bacteriostatic mechanism of phenazine substances against Xoc was investigated through physiological response and transcriptomic analysis.
Results
showed that phenazine substances affects the cell membrane permeability of Xoc, which causes cell swelling and deformation, blockage of flagellum synthesis, and imbalance of intracellular environment. The changes in intracellular environment affect the physiological and metabolic functions of Xoc, which reduces the formation of pathogenic factors and pathogenicity. Through transcriptomic analysis, we found that among differentially expressed genes, the expression of 595 genes was induced significantly (275 up-regulated and 320 down-regulated). In addition, we observed that phenazine substances affects three main functions of Xoc, i.e., transmembrane transporter activity, DNA-mediated transposition, and structural molecular activity. Phenazine substances also inhibits the potassium ion transport system that reduces Xoc resistance and induces the phosphate ion transport system to maintain the stability of the internal environment. Finally, we conclude that phenazine substances could retard cell growth and reduce the pathogenicity of Xoc by affecting cell structure and physiological metabolism. Altogether, our study highlights latest insights into the antibacterial mechanism of phenazine substances against Xoc and provides basic guidance to manage the incidence of bacterial leaf streak of rice.

Citations

Citations to this article as recorded by  
  • Comparative transcriptome analysis reveals molecular mechanisms of resistance in Chinese cabbage to Plasmodiophora brassicae pathotype 11
    Yue Qiu, Jinhao Zhang, Chunju Deng, Jiasheng Yuan, Bowen Wang, Han Meng, Mohamed Mohany, Liting Zeng, Lanfang Wei, Waqar Ahmed, Guanghai Ji
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • Potential of Plant-Based Agents as Next-Generation Plant Growth-Promotors and Green Bactericides Against Pseudomonas savastanoi pv. savastanoi
    Laura Košćak, Janja Lamovšek, Edyta Đermić, Sara Godena
    Agronomy.2025; 15(4): 819.     CrossRef
  • Evaluation the role of Luteibacter pinisoli DP2-30 in mitigating pine wilt disease caused by Bursaphelenchus xylophilus through modulation of host microbiome
    Waqar Ahmed, Wenhua Ye, Jidong Pan, Songsong Liu, Wenxia Ji, Shun Zhou, Fusheng Wang, Zhiguang Li, Mohamed Mohany, Xinrong Wang
    Frontiers in Plant Science.2025;[Epub]     CrossRef
  • Targeted subcellular localization of a novel fungicidal compound N-(naphthalen-1-yl) phenazine-1-carboxamide inhibiting Rhizoctonia solani
    Shuangqing Liu, Ding Wen, Wenhui Jia, Xiaolan Liao, Hu Pan, Ya Zhang, Chong Wang
    Pesticide Biochemistry and Physiology.2025; 213: 106554.     CrossRef
  • Antibacterial activity and mechanism of Myxin from Lysobacter antibioticus against Xanthomonas fragariae
    Chunju Deng, Jinhao Zhang, Yue Qiu, Haowen He, Juxiang Wang, Mengxiang Ma, Yimei Li, Liting Zeng, Jingyuan Luo, Guanghai Ji
    Pest Management Science.2025;[Epub]     CrossRef
  • Biocontrol potential of endophytic Bacillus subtilis A9 against rot disease of Morchella esculenta
    Xue Chen, Yin Zhang, ShengQian Chao, LiLi Song, GuoGan Wu, Yu Sun, YiFan Chen, BeiBei Lv
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • A Novel Plant-Derived Biopesticide Mitigates Fusarium Root Rot of Angelica sinensis by Modulating the Rhizosphere Microbiome and Root Metabolome
    Qi Liu, Waqar Ahmed, Guoli Li, Yilin He, Mohamed Mohany, Zhaoyu Li, Tong Shen
    Plants.2024; 13(16): 2180.     CrossRef
  • Trichoderma Production and Encapsulation Methods for Agricultural Applications
    Erick Vindas-Reyes, Randall Chacón-Cerdas, William Rivera-Méndez
    AgriEngineering.2024; 6(3): 2366.     CrossRef
  • A Novel Dry-Cured Ham Broth-Derived Peptide JHBp2 Effectively Inhibits Salmonella typhimurium In Vitro: Integrated Metabolomic, Proteomic, and Molecular Simulation Analyses
    Ziyi Yang, Zixu Wang, Ruoxin Wang, Wangang Zhang
    Journal of Agricultural and Food Chemistry.2024; 72(25): 14433.     CrossRef
  • Exploring the nematicidal mechanisms and control efficiencies of oxalic acid producing Aspergillus tubingensis WF01 against root-knot nematodes
    Zhong-Yan Yang, Yuan-Chen Dai, Yuan-Qi Mo, Jia-Lun Wang, Li Ma, Pei-Ji Zhao, Ying Huang, Rui-Bin Wang, Wei Li, Salim S. Al-Rejaie, Jian-Jin Liu, Yi Cao, Ming-He Mo
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Identification of the Ilex macrocarpa anthracnose pathogen and the antifungal potential of the cell-free supernatant of Bacillus velezensis against Colletotrichum fioriniae
    Chun Fu, Shushan Wan, Peng Yang, Xizhu Zhao, Yueyao Yan, Shijiao Jiang, Habib Ali
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Transcriptome profiling reveals the impact of various levels of biochar application on the growth of flue-cured tobacco plants
    Yingfen Yang, Waqar Ahmed, Gang Wang, Chenghu Ye, Shichen Li, Meiwei Zhao, Jinhao Zhang, Junjie Wang, Saleh H. Salmen, Lianzhang Wu, Zhengxiong Zhao
    BMC Plant Biology.2024;[Epub]     CrossRef
  • Rice Varieties Intercropping Induced Soil Metabolic and Microbial Recruiting to Enhance the Rice Blast (Magnaporthe Oryzae) Resistance
    Xiao-Qiao Zhu, Mei Li, Rong-Ping Li, Wen-Qiang Tang, Yun-Yue Wang, Xiao Fei, Ping He, Guang-Yu Han
    Metabolites.2024; 14(9): 507.     CrossRef
  • Characterization of a broad-spectrum antifungal strain, Streptomyces graminearus STR-1, against Magnaporthe oryzae
    Wenyuan Shen, Renju Liu, Jiazheng Wang, Maolan Yang, Tuo Qi, Guosong Shu, Min He, Xuewei Chen
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • RETRACTED: Evaluation of the novel endophytic fungus Chaetomium ascotrichoides 1‐24‐2 from Pinus massoniana as a biocontrol agent against pine wilt disease caused by Bursaphelenchus xylophilus
    Md Kamaruzzaman, Lijun Zheng, Shun Zhou, Wenhua Ye, Yongqiang Yuan, Qiu Qi, Yongfeng Gao, Jiajin Tan, Yan Wang, Bingjia Chen, Zhiguang Li, Songsong Liu, Renjun Mi, Ke Zhang, Chen Zhao, Waqar Ahmed, Xinrong Wang
    Pest Management Science.2024; 80(10): 4924.     CrossRef
  • Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry
    Yue Qiu, Fangjun Wei, Han Meng, Menglin Peng, Jinhao Zhang, Yilu He, Lanfang Wei, Waqar Ahmed, Guanghai Ji
    Frontiers in Plant Science.2023;[Epub]     CrossRef
  • Genetic Basis and Expression Pattern Indicate the Biocontrol Potential and Soil Adaption of Lysobacter capsici CK09
    Pu Yang, Chaofan Qu, Miaomiao Yuan, Bo Xi, Xiu Jia, Ben Zhang, Lizhen Zhang
    Microorganisms.2023; 11(7): 1768.     CrossRef
  • Seed coat treatment by plant-growth-promoting rhizobacteria Lysobacter antibioticus 13–6 enhances maize yield and changes rhizosphere bacterial communities
    Zhenlin Dai, Waqar Ahmed, Jun Yang, Xiuying Yao, Jinhao Zhang, Lanfang Wei, Guanghai Ji
    Biology and Fertility of Soils.2023; 59(3): 317.     CrossRef
  • The Antibacterial Effect of Selected Essential Oils and Their Bioactive Constituents on Pseudomonas savastanoi pv. savastanoi: Phytotoxic Properties and Potential for Future Olive Disease Control
    Laura Košćak, Janja Lamovšek, Edyta Đermić, Sara Godena
    Microorganisms.2023; 11(11): 2735.     CrossRef
  • Plant-Microbe Interaction: Mining the Impact of Native Bacillus amyloliquefaciens WS-10 on Tobacco Bacterial Wilt Disease and Rhizosphere Microbial Communities
    Waqar Ahmed, Zhenlin Dai, Jinhao Zhang, Shichen Li, Ayesha Ahmed, Shahzad Munir, Qi Liu, Yujiao Tan, Guanghai Ji, Zhengxiong Zhao, Lindsey Price Burbank
    Microbiology Spectrum.2022;[Epub]     CrossRef
Characterization of a cold-adapted debranching enzyme and its role in glycogen metabolism and virulence of Vibrio vulnificus MO6-24/O
Ah-Reum Han , Haeyoung Kim , Jong-Tae Park , Jung-Wan Kim
J. Microbiol. 2022;60(4):375-386.   Published online February 14, 2022
DOI: https://doi.org/10.1007/s12275-022-1507-3
  • 343 View
  • 0 Download
  • 5 Web of Science
  • 5 Crossref
AbstractAbstract PDF
Vibrio vulnificus MO6-24/O has three genes annotated as debranching enzymes or pullulanase genes. Among them, the gene encoded by VVMO6_03032 (vvde1) shares a higher similarity at the amino acid sequence level to the glycogen debranching enzymes, AmyX of Bacillus subtilis (40.5%) and GlgX of Escherichia coli (55.5%), than those encoded by the other two genes. The vvde1 gene encoded a protein with a molecular mass of 75.56 kDa and purified Vvde1 efficiently hydrolyzed glycogen and pullulan to shorter chains of maltodextrin and maltotriose (G3), respectively. However, it hydrolyzed amylopectin and soluble starch far less efficiently, and β-cyclodextrin (β-CD) only rarely. The optimal pH and temperature of Vvde1 was 6.5 and 25°C, respectively. Vvde1 was a cold-adapted debranching enzyme with more than 60% residual activity at 5°C. It could maintain stability for 2 days at 25°C and 1 day at 35°C, but it destabilized drastically at 40°C. The Vvde1 activity was inhibited considerably by Cu2+, Hg2+, and Zn2+, while it was slightly enhanced by Co2+, Ca2+, Ni2+, and Fe2+. The vvde1 knock-out mutant accumulated more glycogen than the wild-type in media supplemented with 1.0% maltodextrin; however, the side chain length distribution of glycogen was similar to that of the wild-type except G3, which was much more abundant in the mutant. Therefore, Vvde1 seemed to debranch glycogen with the degree of polymerization 3 (DP3) as the specific target branch length. Virulence of the pathogen against Caenorhabditis elegans was attenuated significantly by the vvde1 mutation. These results suggest that Vvde1 might be a unique glycogen debranching enzyme that is involved in both glycogen utilization and shaping of glycogen molecules, and contributes toward virulence of the pathogen.

Citations

Citations to this article as recorded by  
  • Characterization of glycogen-related glycoside hydrolase glgX and glgB from Klebsiella pneumoniae and their roles in biofilm formation and virulence
    Xinyue Liu, Jialin Li, Ruibing Wu, Liping Bai
    Frontiers in Cellular and Infection Microbiology.2024;[Epub]     CrossRef
  • Function of the mdxR gene encoding a novel regulator for carbohydrate metabolism and sporulation in Bacillus subtilis 168
    Tianshi Wang, Jung-Wan Kim
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Identification of a novel cyclomaltodextrinase annotated as a neopullulanase in the genome of Bacillus cereus
    Bo-Ram Park, Davoodbasha MubarakAli, Jung-Wan Kim
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
    Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
    PLOS ONE.2023; 18(12): e0289072.     CrossRef
  • Functional characterization of maltodextrin glucosidase for maltodextrin and glycogen metabolism in Vibrio vulnificus MO6-24/O
    Hye-Young Kim, MubarakAli Davoodbasha, Jung-Wan Kim
    Archives of Microbiology.2022;[Epub]     CrossRef
Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates
Aeryun Kim , Jing Lai , D. Scott Merrell , Ji-Hye Kim , Hanfu Su , Jeong-Heon Cha
J. Microbiol. 2021;59(12):1125-1132.   Published online October 31, 2021
DOI: https://doi.org/10.1007/s12275-021-1450-8
  • 345 View
  • 0 Download
  • 4 Web of Science
  • 3 Crossref
AbstractAbstract PDF
Helicobacter pylori outer membrane inflammatory protein A (OipA) was originally named for its role in inducing inflammation in the host, as evidenced by high mucosal IL-8 levels. Expression of OipA is regulated by phase variation of a CT dinucleotide-repeat located in the 5􍿁􀁇region of the gene. However, little is known about OipA geographic diversity across isolates. To address this gap, we conducted a large-scale molecular epidemiologic analysis using H. pylori clinical isolates obtained from two geographically distinct populations: Korea and the United States (US). Most Korean isolates (98.7%) possessed two copies of oipA located at two specific loci (A and B) while all US isolates contained only one copy of oipA at locus A. Furthermore, most Korean oipA (94.8%) possessed three or less CT repeats while most US oipA (96.6%) contained five or more CT repeats. Among the two copies, all Korean H. pylori possessed at least one oipA ‘on’ phase variant while the single copy of oipA in US isolates showed 56.2% ‘on’ and 43.8% ‘off.’ Thus, host differences seem to have driven geographic diversification of H. pylori across these populations such that OipA expression in US isolates is still regulated by phase variation with 5 or more CT repeats, while Korean isolates always express OipA; duplication of the oipA combined with a reduction of CT repeats to three or less ensures continued expression. En masse, these findings suggest that diversity in the oipA gene copy number, CT repeats, and phase variation among H. pylori from different populations may confer a benefit in adaptation to particular host populations.

Citations

Citations to this article as recorded by  
  • Pathogenicity and virulence of Helicobacter pylori : A paradigm of chronic infection
    Marguerite Clyne, Tadhg Ó Cróinín
    Virulence.2025;[Epub]     CrossRef
  • Genetic diversity of the oipA gene among Helicobacter pylori isolates and clinical outcome in Vietnam
    Thi Hong Nhung Thai, Hong Phong Nguyen, Thi Hai Yen Nguyen, Thi Be Hai Nguyen, Thai Hoa Nguyen, Thi Mai Ngan Nguyen, Thi Minh Thi Ha
    Infection, Genetics and Evolution.2023; 112: 105438.     CrossRef
  • Characterization of East-Asian Helicobacter pylori encoding Western EPIYA-ABC CagA
    Kavinda Tissera, Myeong-A Kim, Jing Lai, Sacheera Angulmaduwa, Aeryun Kim, D. Scott Merrell, Ji-Hye Kim, Hanfu Su, Jeong-Heon Cha
    Journal of Microbiology.2022; 60(2): 207.     CrossRef
The transcription factor Cas5 suppresses hyphal morphogenesis during yeast-form growth in Candida albicans
Jong-Myeong Kim , Hye Yun Moon , Dong Wook Lee , Hyun Ah Kang , Jeong-Yoon Kim
J. Microbiol. 2021;59(10):911-919.   Published online September 7, 2021
DOI: https://doi.org/10.1007/s12275-021-1326-y
  • 312 View
  • 0 Download
  • 3 Web of Science
  • 2 Crossref
AbstractAbstract PDF
Candida albicans is an opportunistic human pathogen that exists as yeast, hyphal or pseudohyphal forms depending on pH, nutrients, and temperature. The morphological transition from yeast to hyphae, which is required for the complete virulence of C. albicans, is controlled by many transcription factors that activate or repress hypha-specific genes. The C. albicans transcriptional factor Cas5, a key regulator of genes involved in cell wall integrity, affects the susceptibility of C. albicans to fluconazole, an inhibitor of ergosterol synthesis. In this study, we found that deletion of CAS5 in C. albicans decreased the expression levels of a set of ergosterol biosynthesis genes, such as ERG2, ERG3, ERG5, ERG6, ERG11, and ERG24,
result
ing in the accumulation of lanosterol and zymosterol, which are intermediate metabolites in the ergosterol biosynthesis pathway. Interestingly, it was observed that the cas5Δ/Δ mutant could not maintain the yeast form under non-hyphainducing conditions, while the CAS5-overexpressing cells could not form hyphae under hypha-inducing conditions. Consistent with these observations, the cas5Δ/Δ mutant highly expressed hypha-specific genes, ALS3, ECE1, and HWP1, under non-hypha-inducing conditions. In addition, CAS5 transcription was significantly downregulated immediately after hyphal initiation in the wild-type strain. Furthermore, the cas5Δ/Δ mutant reduced the transcription of NRG1, which encodes a major repressor of hyphal morphogenesis, while Cas5 overexpression increased the transcription of NRG1 under hyphainducing conditions. Collectively, this study suggests the potential role of Cas5 as a repressor of hypha-specific genes during yeast-form growth of C. albicans.

Citations

Citations to this article as recorded by  
  • Cas5 Regulates the Exposure of β-Glucan, the Cell Surface Hydrophobicity, and the Expression of Cell Wall Proteins to Remodel the Candida albicans Cell Wall and Participates in the Recruitment of Neutrophils
    Qiyue Zhang, Guanglin Li, Yanmei Wang, Chen Yang, Wenhui Bai, Qingqing Li, Jiye Zhang, Peipei Zhang
    Microorganisms.2025; 13(3): 683.     CrossRef
  • The Role of Sfp1 in Candida albicans Cell Wall Maintenance
    Che-Kang Chang, Min-Chi Yang, Hsueh-Fen Chen, Yi-Ling Liao, Chung-Yu Lan
    Journal of Fungi.2022; 8(11): 1196.     CrossRef
CagL polymorphisms between East Asian and Western Helicobacter pylori are associated with different abilities to induce IL-8 secretion
Yun Hui Choi , Jing Lai , Myeong-A Kim , Aeryun Kim , Jinmoon Kim , Hanfu Su , Linhu Ge , Jeong-Heon Cha
J. Microbiol. 2021;59(8):763-770.   Published online June 1, 2021
DOI: https://doi.org/10.1007/s12275-021-1136-2
  • 335 View
  • 0 Download
  • 6 Web of Science
  • 4 Crossref
AbstractAbstract PDF
Helicobacter pylori colonizes human gastric mucosa. Its infection is associated with gastric diseases including gastric cancer. CagA is one of the most important toxins produced by H. pylori. It is related to gastric cancer which can be injected into host cells via a type IV secretion system (T4SS). CagL is a structural component of T4SS apparatus, which triggers host cell signaling pathway. It has been reported that CagL polymorphisms may influence the severity of disease development. To explore the contribution of CagL polymorphisms between East Asian and Western H. pylori in pathogenesis, cagL gene in G27 H. pylori was swapped by K74 cagL which is identical to East Asian CagL consensus sequence and by Western 26695 H. pylori, resulting in G27ΔcagL/cagLK74 and G27ΔcagL/cagL26695, respectively. Intriguingly, G27ΔcagL/ cagLK74 showed significantly less ability of IL-8 induction than G27ΔcagL/cagL26695 while displayed similar abilities of CagA phosphorylation, and cell elongation. Taken together, this study suggests that the CagL polymorphism may influence IL-8 induction, and K74 CagL has less ability to induce IL-8 secretion than G27 or 26695 CagL. Further research should address how the different capabilities of IL-8 induction between intraspecies-CagL are associated with the large differences of the incidence of gastric cancer between East Asian and Western countries.

Citations

Citations to this article as recorded by  
  • Roles of the components of the cag -pathogenicity island encoded type IV secretion system in Helicobacter pylori
    Lingzhu Gou, Xiaoping Yang, Jianwei Yun, Zenghui Ma, Xiaofeng Zheng, Hongwei Du, Dekui Zhang
    Future Microbiology.2024; 19(14): 1253.     CrossRef
  • Antibacterial and Immunoregulatory Effects of Metformin against Helicobacter pylori Infection in Rat Model
    Hassan Valadbeigi, Saeed Khoshnood, Babak Negahdari, Mohd Azmuddin Abdullah, Mohammad Hossein Haddadi, Abhimanyu Abhimanyu
    BioMed Research International.2023;[Epub]     CrossRef
  • New CagL Amino Acid Polymorphism Patterns of Helicobacter pylori in Peptic Ulcer and Non-Ulcer Dyspepsia
    Reyhan Caliskan, Silva Polat Sari, Bahadir Ercan, Kivanc Derya Peker, Mehtap Omac Sonmez, Ozer Akgul, Burcu Sapmaz, Aliye Soylu, Gokhan Tolga Adas, Yasar Ali Oner, Pelin Yuksel Mayda
    Medicina.2022; 58(12): 1738.     CrossRef
  • Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates
    Aeryun Kim, Jing Lai, D. Scott Merrell, Ji-Hye Kim, Hanfu Su, Jeong-Heon Cha
    Journal of Microbiology.2021; 59(12): 1125.     CrossRef
The quorum sensing regulator OpaR is a repressor of polar flagellum genes in Vibrio parahaemolyticus
Renfei Lu , Junfang Sun , Yue Qiu , Miaomiao Zhang , Xingfan Xue , Xue Li , Wenhui Yang , Dongsheng Zhou , Lingfei Hu , Yiquan Zhang
J. Microbiol. 2021;59(7):651-657.   Published online June 1, 2021
DOI: https://doi.org/10.1007/s12275-021-0629-3
  • 331 View
  • 0 Download
  • 30 Web of Science
  • 31 Crossref
AbstractAbstract PDF
Vibrio parahaemolyticus possesses two types of flagella: a single polar flagellum (Pof) for swimming and the peritrichous lateral flagella (Laf) for swarming. Expression of Laf genes has previously been reported to be regulated by the quorum sensing (QS) regulators AphA and OpaR. In the present study, we showed that OpaR, the QS regulator at high cell density (HCD), acted as a negative regulator of swimming motility and the transcription of Pof genes in V. parahaemolyticus. OpaR bound to the promoter-proximal DNA regions of flgAMN, flgMN, and flgBCDEFGHIJ within the Pof gene loci to repress their transcription, whereas it negatively regulates the transcription of flgKL-flaC in an indirect manner. Thus, this work investigated how QS regulated the swimming motility via direct action of its master regulator OpaR on the transcription of Pof genes in V. parahaemolyticus.

Citations

Citations to this article as recorded by  
  • H-NS-Mediated Regulation of Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus
    Yue Zhou, Jingyang Chang, Feng Li, Mei He, Rui Li, Yaqin Hou, Yiquan Zhang, Renfei Lu, Ming Yang
    Current Microbiology.2025;[Epub]     CrossRef
  • GefB, a GGDEF domain-containing protein, affects motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing regulators
    Yining Zhou, Jingyang Chang, Miaomiao Zhang, Xue Li, Xi Luo, Wanpeng Li, Zhukang Tian, Nan Zhang, Bin Ni, Yiquan Zhang, Renfei Lu
    Gene.2025; 933: 148968.     CrossRef
  • GepA, a GGDEF-EAL protein, regulates biofilm formation and swimming motility in Vibrio parahaemolyticus
    Miaomiao Zhang, Yurui Zhu, Xue Li, Xi Luo, Hui Sun, Shuhui Xiong, Renfei Lu, Yiquan Zhang
    Archives of Microbiology.2025;[Epub]     CrossRef
  • Sublethal Curcumin Exposure Induces Global Gene Expression and Biofilm-Related Phenotypic Changes in Vibrio parahaemolyticus
    Lili Huang, Miaomiao Zhang, Xi Luo, Xue Li, Yiquan Zhang, Renfei Lu
    Current Microbiology.2025;[Epub]     CrossRef
  • Temperature Influences Antimicrobial Resistance and Virulence of Vibrio parahaemolyticus Clinical Isolates from Quebec, Canada
    Feriel C. Mahieddine, Annabelle Mathieu-Denoncourt, Marylise Duperthuy
    Pathogens.2025; 14(6): 521.     CrossRef
  • The coordinated regulatory impact of AcsS and TpdA on biofilm formation in Vibrio parahaemolyticus
    Bin Ni, Jingyang Chang, Yining Zhou, Wanpeng Li, Zhukang Tian, Renfei Lu, Yiquan Zhang
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • Synergistic effects of biofloc and the probiotic Pseudoalteromonas piscicida 1Ub on suppression of virulence gene expression in Vibrio parahaemolyticus and immunity enhancement in Pacific white shrimp
    Meidevi Ratna Styaningrum, Widanarni, Munti Yuhana, Muhamad Gustilatov
    Microbial Pathogenesis.2025; 207: 107899.     CrossRef
  • The effect of environmental calcium on gene expression, biofilm formation and virulence of Vibrio parahaemolyticus
    Xue Li, Jingyang Chang, Miaomiao Zhang, Yining Zhou, Tingting Zhang, Yiquan Zhang, Renfei Lu
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • VPA0198, a GGDEF domain-containing protein, affects the motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing associated regulators
    Yining Zhou, Jingyang Chang, Miaomiao Zhang, Xue Li, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bin Ni, Renfei Lu, Yiquan Zhang
    Microbial Pathogenesis.2024; 195: 106882.     CrossRef
  • Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus
    F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, A. Alexis Lopez-Zavala
    F1000Research.2024; 12: 1256.     CrossRef
  • Environmental magnesium ion affects global gene expression, motility, biofilm formation and virulence of Vibrio parahaemolyticus
    Xue Li, Xiaobai Zhang, Miaomiao Zhang, Xi Luo, Tingting Zhang, Xianjin Liu, Renfei Lu, Yiquan Zhang
    Biofilm.2024; 7: 100194.     CrossRef
  • The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842
    Baiyuan Li, Songwei Ni, Yabo Liu, Jianzhong Lin, Xiaoxue Wang
    Microbiological Research.2024; 286: 127817.     CrossRef
  • The Impact of Vp-Porin, an Outer Membrane Protein, on the Biological Characteristics and Virulence of Vibrio Parahaemolyticus
    Jinyuan Che, Qitong Fang, Shaojie Hu, Binghong Liu, Lei Wang, Xiu Fang, Lekang Li, Tuyan Luo, Baolong Bao
    Biology.2024; 13(7): 485.     CrossRef
  • Phenotypic changes and gene expression profiles of Vibrio parahaemolyticus in response to low concentrations of ampicillin
    Xi Luo, Miaomiao Zhang, Yiquan Zhang, Xue Li, Renfei Lu
    The Journal of Antibiotics.2024; 77(12): 823.     CrossRef
  • Bioprospecting and Exploration of Phytochemicals as Quorum Sensing Inhibitors against Cariogenic Dental Biofilm
    S. Arya, R. Usha
    Journal of Pure and Applied Microbiology.2024; 18(1): 100.     CrossRef
  • Identification of an LysR family transcriptional regulator that activates motility and flagellar gene expression in Vibrio parahaemolyticus
    Jingyang Chang, Yining Zhou, Xue Li, Miaomiao Zhang, Yiquan Zhang, Bin Ni, Renfei Lu
    Letters in Applied Microbiology.2024;[Epub]     CrossRef
  • The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces
    Francis J. Santoriello, Bonnie L. Bassler, Ankur B. Dalia
    PLOS Genetics.2024; 20(7): e1011243.     CrossRef
  • Evaluation of Therapeutic Efficiency of Stylicin against Vibrio parahaemolyticus Infection in Shrimp Penaeus vannamei through Comparative Proteomic Approach
    Saranya Chakrapani, Akshaya Panigrahi, Esakkiraj Palanichamy, Sathish Kumar Thangaraj, Naveenkumar Radhakrishnan, Puspamitra Panigrahi, Radhakrishnan Nagarathnam
    Probiotics and Antimicrobial Proteins.2024; 16(1): 76.     CrossRef
  • CalR Inhibits the Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus
    Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Haisheng Wu, Renfei Lu, Yiquan Zhang
    Journal of Microbiology.2024; 62(12): 1125.     CrossRef
  • Quorum Sensing: An Emerging Role for Vibrio Infection and Host Defense
    Hao-Nan Lin, Xian-Hui Huang, Xin-Jun Miao, Wei-Lin Hu, Yong-Liang Lou, Dan-Li Xie
    Infectious Microbes and Diseases.2024; 6(2): 47.     CrossRef
  • QsvR and OpaR coordinately repress biofilm formation by Vibrio parahaemolyticus
    Miaomiao Zhang, Xingfan Xue, Xue Li, Qimin Wu, Tingting Zhang, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Renfei Lu, Yiquan Zhang
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation
    Yiquan Zhang, Tingting Zhang, Yue Qiu, Miaomiao Zhang, Xiuhui Lu, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bo Gao, Renfei Lu
    Current Microbiology.2023;[Epub]     CrossRef
  • Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus
    F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, A. Alexis Lopez-Zavala
    F1000Research.2023; 12: 1256.     CrossRef
  • Effect of sublethal dose of chloramphenicol on biofilm formation and virulence in Vibrio parahaemolyticus
    Miaomiao Zhang, Liyan Cai, Xi Luo, Xue Li, Tingting Zhang, Fei Wu, Yiquan Zhang, Renfei Lu
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Quorum sensing and QsvR tightly control the transcription of vpa0607 encoding an active RNase II-type protein in Vibrio parahaemolyticus
    Yiquan Zhang, Xingfan Xue, Fengjun Sun, Xue Li, Miaomiao Zhang, Qimin Wu, Tingting Zhang, Xi Luo, Renfei Lu
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • QsvR represses the transcription of polar flagellum genes in Vibrio parahaemolyticus
    Miaomiao Zhang, Xingfan Xue, Xue Li, Xi Luo, Qimin Wu, Tingting Zhang, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Renfei Lu, Yiquan Zhang
    Microbial Pathogenesis.2023; 174: 105947.     CrossRef
  • Transcriptomic Analysis of Vibrio parahaemolyticus Underlying the Wrinkly and Smooth Phenotypes
    Qimin Wu, Xue Li, Tingting Zhang, Miaomiao Zhang, Xingfan Xue, Wenhui Yang, Lingfei Hu, Zhe Yin, Dongsheng Zhou, Yuyu Sun, Renfei Lu, Yiquan Zhang, Sébastien P. Faucher
    Microbiology Spectrum.2022;[Epub]     CrossRef
  • Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains
    Masa-aki Yoshida, Takuma Tanabe, Hideo Akiyoshi, Makoto Kawamukai
    Scientific Reports.2022;[Epub]     CrossRef
  • Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus
    Nur Afiqah Md Yusof, Siti Aisyah Razali, Azyyati Mohd Padzil, Benjamin Yii Chung Lau, Syarul Nataqain Baharum, Nor Azlan Nor Muhammad, Nurul Hanun Ahmad Raston, Chou Min Chong, Natrah Fatin Mohd Ikhsan, Magdalena Lenny Situmorang, Low Chen Fei
    Biology.2022; 11(11): 1600.     CrossRef
  • An Increase of Seawater Temperature Upregulates the Expression of Vibrio parahaemolyticus Virulence Factors Implicated in Adhesion and Biofilm Formation
    Mélanie Billaud, François Seneca, Eric Tambutté, Dorota Czerucka
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • Characterization of the RpoN regulon reveals the regulation of motility, T6SS2 and metabolism in Vibrio parahaemolyticus
    Dan Gu, Youkun Zhang, Kangru Wang, Mingzhu Li, Xinan Jiao
    Frontiers in Microbiology.2022;[Epub]     CrossRef
Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
Ye-Seul Lim , Ju-Hee Choi , Kyu-Jin Ahn , Min-Ku Kim , Sung-Ho Bae
J. Microbiol. 2021;59(4):401-409.   Published online March 29, 2021
DOI: https://doi.org/10.1007/s12275-021-1076-x
  • 226 View
  • 0 Download
AbstractAbstract PDF
Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter (HXT) genes in Saccharomyces cerevisiae. They can potentially recombine via single-strand annealing (SSA) pathway. SSA between highly divergent sequences generates heteroduplex DNA intermediates with many mismatches, which can be corrected by mismatch repair (MMR), resulting in recombinant sequences with a single junction point. In this report, we demonstrate that SSA between HXT1 and HXT4 genes in MMR-deficient yeast cells produces recombinant genes with multiple-junctions resulting from alternating HXT1 and HXT4 tracts. The mutations in MMR genes had differential effects on SSA frequencies; msh6Δ mutation significantly stimulated SSA events, whereas msh2Δ and msh3Δ slightly suppressed it. We set up an assay that can identify a pair of recombinant genes derived from a single heteroduplex DNA. As a result, the recombinant genes with multiple-junctions were found to accompany genes with single-junctions. Based on the results presented here, a model was proposed to generate multiple-junctions in SSA pathway involving an alternative short-patch repair system.
Functional and structural characterization of Deinococcus radiodurans R1 MazEF toxin-antitoxin system, Dr0416-Dr0417
Immanuel Dhanasingh , Eunsil Choi , Jeongeun Lee , Sung Haeng Lee , Jihwan Hwang
J. Microbiol. 2021;59(2):186-201.   Published online February 1, 2021
DOI: https://doi.org/10.1007/s12275-021-0523-z
  • 316 View
  • 0 Download
  • 6 Web of Science
  • 4 Crossref
AbstractAbstract PDF
In prokaryotes, toxin-antitoxin (TA) systems are commonly found. They likely reflect the adaptation of pathogenic bacteria or extremophiles to various unfavorable environments by slowing their growth rate. Genomic analysis of the extremophile Deinococcus radiodurans R1 revealed the presence of eight type II TA systems, including the genes dr0417, dr0660, dr1530, dr0690, and dr1807. Expression of these toxin genes led to inhibition of Escherichia coli growth, whereas their antidote antitoxins were able to recover the growth defect. Remarkably, Dr0417 (DrMazF) showed endoribonuclease activity toward rRNAs as well as mRNAs, as determined by in vivo and in vitro RNA cleavage assays, and this activity was inhibited by Dr0416 (DrMazE). It was also found that the expression of dr0416-0417 module is directly regulated by the DrMazE-MazF complex. Furthermore, this TA module was induced under stress conditions and plays an important role in survival. To understand the regulatory mechanism at the molecular level, we determined the first high-resolution structures of DrMazF alone and of the DrMazE-MazF complex. In contrast with the hetero-hexameric state of typical MazEMazF complexes found in other species, DrMazE-MazF crystal structure consists of a hetero-trimer, with the DNA-binding domain of DrMazE undergoing self-cleavage at the flexible linker loop. Our structure revealed that the unique residue R54 provides an additional positive charge to the substratebinding pocket of DrMazF, its mutation significantly affects the endonuclease activity. Thus, our work reports the unique structural and biochemical features of the DrMazE-MazF system.

Citations

Citations to this article as recorded by  
  • SeaMoon: From protein language models to continuous structural heterogeneity
    Valentin Lombard, Dan Timsit, Sergei Grudinin, Elodie Laine
    Structure.2025; 33(9): 1577.     CrossRef
  • Focused Overview of Mycobacterium tuberculosis VapBC Toxin–Antitoxin Systems Regarding Their Structural and Functional Aspects: Including Insights on Biomimetic Peptides
    Sung-Min Kang
    Biomimetics.2023; 8(5): 412.     CrossRef
  • Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642
    Eunsil Choi, Ahhyun Huh, Changmin Oh, Jeong-Il Oh, Ho Young Kang, Jihwan Hwang
    Journal of Microbiology.2022; 60(2): 192.     CrossRef
  • Identification and characterization of the type II toxin-antitoxin systems in the carbapenem-resistant Acinetobacter baumannii
    Alireza Japoni-Nejad, Elnaz Harifi Mood, Parastoo Ehsani, Soroush Sardari, Fatemah Sadeghpour Heravi, Saeid Bouzari, Nader Shahrokhi
    Microbial Pathogenesis.2021; 158: 105052.     CrossRef
Spot 42 RNA regulates putrescine catabolism in Escherichia coli by controlling the expression of puuE at the post-transcription level
Xin Sun , Ruyan Li , Guochen Wan , Wanli Peng , Shuangjun Lin , Zixin Deng , Rubing Liang
J. Microbiol. 2021;59(2):175-185.   Published online February 1, 2021
DOI: https://doi.org/10.1007/s12275-021-0421-4
  • 333 View
  • 0 Download
  • 2 Web of Science
  • 2 Crossref
AbstractAbstract PDF
Putrescine, a typical polyamine compound important for cell growth and stress resistance, can be utilized as an energy source. However, the regulation of its catabolism is unclear. Here the small RNA (sRNA) Spot 42, an essential regulator of carbon catabolite repression (CCR), was confirmed to participate in the post-transcriptional regulation of putrescine catabolism in Escherichia coli. Its encoding gene spf exclusively exists in the γ-proteobacteria and contains specific binding sites to the 5􍿁-untranslated regions of the puuE gene, which encodes transaminase in the glutamylated putrescine pathway of putrescine catabolism converting γ-aminobutyrate (GABA) into succinate semialdehyde (SSA). The transcription of the spf gene was induced by glucose, inhibited by putrescine, and unaffected by PuuR, the repressor of puu genes. Excess Spot 42 repressed the expression of PuuE significantly in an antisense mechanism through the direct and specific base-pairing between the 51–57 nt of Spot 42 and the 5􍿁- UTR of puuE. Interestingly, Spot 42 mainly influenced the stability of the puuCBE transcript. This work revealed the regulatory role of Spot 42 in putrescine catabolism, in the switch between favorable and non-favorable carbon source utilization, and in the balance of metabolism of carbon and nitrogen sources.

Citations

Citations to this article as recorded by  
  • Regulation of TCA cycle genes by srbA sRNA: Impacts on Pseudomonas aeruginosa virulence and survival
    Piyali Saha, Samir Kumar Mukherjee, Sk Tofajjen Hossain
    Biochemical and Biophysical Research Communications.2024; 737: 150520.     CrossRef
  • Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression
    Jun Ren, Nuong Thi Nong, Phuong N. Lam Vo, Hyang-Mi Lee, Dokyun Na
    ACS Synthetic Biology.2024; 13(10): 3256.     CrossRef
Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea
Yang Liu , Juan Du , Jun Zhang , Qiliang Lai , Zongze Shao , Honghui Zhu
J. Microbiol. 2020;58(2):92-98.   Published online January 29, 2020
DOI: https://doi.org/10.1007/s12275-020-9405-z
  • 375 View
  • 0 Download
  • 8 Web of Science
  • 9 Crossref
AbstractAbstract PDF
A Gram-stain-negative, strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South China Sea. Strain HSLHS9T could grow at 15–41°C (optimum 28°C), at pH 5.0–9.0 (optimum 6.0–7.0), and in 0–7% (w/v) NaCl (optimum 2–3%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HSLHS9T shared high identities with the closely related Parahaliea aestuarii S2-26T (98.6%) and Parahaliea mediterranea 7SM29T (97.8%) and formed a distinct lineage within the genus Parahaliea. Wholegenome sequencing of strain HSLHS9T revealed the size of 4.8 Mbp and DNA G + C content of 61.8 mol%. Strain HSLHS9T shared the digital DNA-DNA hybridization values of 22.4% and 23.0%, and the average nucleotide identities of 79.7% and 79.9%, respectively, with the two type strains above. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C17:1 ω8c, and C16:0. The sole isoprenoid quinone was identified as Q-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminolipid, and two glycolipids. Based on taxonomic data obtained in this study, it is suggested that strain HSLHS9T represents a novel species of the genus Parahaliea, for which the name Parahaliea maris sp. nov. is proposed. The type strain is HSLHS9T (= MCCC 1A06717T = KCTC 52307T). An emended description of the genus Parahaliea is also provided.

Citations

Citations to this article as recorded by  
  • Identification of Roseomonas xinghualingensis sp. nov. isolated from hospital air
    Zhiming Kang, Wenjing Lei, Ji Pu, Lijun Zhao, Guowen Min, Yufeng Liu, Wenjuan Chang, Yuqian Gao, Kui Dong, Bin Sun
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
  • A comparative analysis of the microbial communities and functional genes of the nitrogen cycling in mangroves of China, Indian and Malaysia
    Zhihui Qian, Yuyang Li, Amit Pratush, Jie Kan, Ji-Dong Gu, Tao Peng, Tongwang Huang, Zhong Hu
    International Biodeterioration & Biodegradation.2024; 190: 105767.     CrossRef
  • Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov.
    Pravin Kumar, Ashish Verma, Pooja Yadav, Joyasree Das, Lalit Kumar, Srinivasan Krishnamurthi
    Science of The Total Environment.2024; 933: 172995.     CrossRef
  • Abundant and rare bacteria in anthropogenic estuary: Community co-occurrence and assembly patterns
    Ziyue Shi, Lili Ma, Yingying Wang, Jie Liu
    Ecological Indicators.2023; 146: 109820.     CrossRef
  • Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
    Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
    Journal of Microbiology.2022; 60(2): 137.     CrossRef
  • Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment
    Shan Jiang, Feng-Bai Lian, You-Yang Sun, Xiao-Kui Zhang, Zong-Jun Du
    International Journal of Systematic and Evolutionary Microbiology .2021;[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.2020; 70(5): 2960.     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
  • Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
    Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
    Journal of Microbiology.2020; 58(6): 463.     CrossRef
Sutterella faecalis sp. nov., isolated from human faeces
Byeong Seob Oh , Ji-Sun Kim , Seung Yeob Yu , Seoung Woo Ryu , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Seung-Hyeon Choi , Kook-Il Han , Keun Chul Lee , Mi Kyung Eom , Min Kuk Suh , Han Sol Kim , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Jung-Sook Lee , Ju Huck Lee
J. Microbiol. 2020;58(2):99-104.   Published online January 29, 2020
DOI: https://doi.org/10.1007/s12275-020-9396-9
  • 333 View
  • 0 Download
  • 7 Web of Science
  • 7 Crossref
AbstractAbstract PDF
An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).

Citations

Citations to this article as recorded by  
  • In vitro gastrointestinal digestion and colonic fermentation of Mangiferin: Impacts on gut microbiota and metabolite profiles
    Huilin Deng, Yaozhong Zheng, Qiongyao Wang, Jiaqi Peng, Weibin Bai, Lingmin Tian, Zouyan He, Rui Jiao
    Journal of Functional Foods.2025; 124: 106667.     CrossRef
  • An Analysis of the Digestive and Reproductive Tract Microbiota in Infertile Women with Obesity
    Jose Bellver, Marta Gonzalez-Monfort, Sandra González, Bruno Toson, Elena Labarta, Gemma Castillón, Giulia Mariani, Carmina Vidal, Juan Giles, Fabio Cruz, Agustin Ballesteros, Marcos Ferrando, Juan Antonio García-Velasco, Diana Valbuena, Felipe Vilella, M
    International Journal of Molecular Sciences.2024; 25(23): 12600.     CrossRef
  • Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023
    Arianna Carella, Karen C. Carroll, Erik Munson, Romney M. Humphries
    Journal of Clinical Microbiology.2024;[Epub]     CrossRef
  • Short-chain fatty acids: Important components of the gut-brain axis against AD
    Yan Huang, Yi Feng Wang, Jing Miao, Rui Fang Zheng, Jin Yao Li
    Biomedicine & Pharmacotherapy.2024; 175: 116601.     CrossRef
  • Bioinformatic Analysis of Sulfotransferases from an Unexplored Gut Microbe, Sutterella wadsworthensis 3_1_45B: Possible Roles towards Detoxification via Sulfonation by Members of the Human Gut Microbiome
    Lauryn Langford, Dhara D. Shah
    International Journal of Molecular Sciences.2024; 25(5): 2983.     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
  • Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens
    Jiali Wei, Huanwei Xiao, Yingbo Wei, Ivan Stève Nguepi Tsopmejio, Chang Sun, Haoyuan Wu, Zhouyu Jin, Hui Song, Suzanne Lynn Ishaq, Yunhe Xu
    mSystems.2023;[Epub]     CrossRef
Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
Lingmin Jiang , Chan Ju Lim , Song-Gun Kim , Jae Cheol Jeong , Cha Young Kim , Dae-Hyuk Kim , Suk Weon Kim , Jiyoung Lee
J. Microbiol. 2020;58(1):24-29.   Published online November 25, 2019
DOI: https://doi.org/10.1007/s12275-020-9346-6
  • 335 View
  • 2 Download
  • 12 Web of Science
  • 12 Crossref
AbstractAbstract PDF
Strain ATSA2T was isolated from surface-sterilized kimchi cabbage (Brassica rapa subsp. pekinensis) seeds and represents a novel bacterium based on the polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ATSA2T formed a lineage within genus Saccharibacillus and was most closely to Saccharibacillus deserti WLG055T (98.1%) and Saccharibacillus qingshengii H6T (97.9%). The whole-genome of ATSA2T comprised a 5,619,468 bp of circular chromosome with 58.4% G + C content. The DNA-DNA relatedness values between strain ATSA2T and its closely related type strains S. deserti WLJ055T and S. qingshengii H6T were 26.0% and 24.0%, respectively. Multiple gene clusters associated with plant growth promotion activities (stress response, nitrogen and phosphorus metabolism, and auxin biosynthesis) were annotated in the genome. Strain ATSA2T was Gram-positive, endospore-forming, facultatively anaerobic, and rod-shaped. It grew at 15–37°C (optimum 25°C), pH 6.0–10.0 (optimum pH 8.0), and in the presence of 0–5% (w/v) NaCl (optimum 1%). The major cellular fatty acids (> 10%) of strain ATSA2T were anteiso- C15:0 and C16:0. MK-7 was the major isoprenoid quinone. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, and three unknown glycolipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, strain ATSA2T is proposed to represent a novel species of genus Saccharibacillus, for which the name is Saccharibacillus brassicae sp. nov. The type strain is ATSA2T (KCTC 43072T = CCTCC AB 2019223T).

Citations

Citations to this article as recorded by  
  • Comprehensive genomic and phenotypic characterization of thermophilic bacterium Sinimarinibacterium thermocellulolyticum sp. nov. HSW-8T, a cellulase-producing bacterium isolated from hot spring water in South Korea
    Yue Jiang, Zhun Li
    Antonie van Leeuwenhoek.2025;[Epub]     CrossRef
  • Improving plant salt tolerance through Algoriphagus halophytocola sp. nov., isolated from the halophyte Salicornia europaea
    Yuxin Peng, Dong Hyun Cho, Zalfa Humaira, Yu Lim Park, Ki Hyun Kim, Cha Young Kim, Jiyoung Lee
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Dasania phycosphaerae sp. nov., isolated from phytoplankton sample from the south coast of the Republic of Korea
    Yue Jiang, Yong Guan, Sungmo Kang, Mi-Kyung Lee, Ki-Hyun Kim, Zhun Li
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T
    Lingmin Jiang, Jiyoon Seo, Yuxin Peng, Doeun Jeon, Soon Ju Park, Cha Young Kim, Pyoung Il Kim, Chul Hong Kim, Ju Huck Lee, Jiyoung Lee
    AMB Express.2023;[Epub]     CrossRef
  • Emticicia fluvialis sp. nov., a potential hormone-degrading bacterium isolated from Nakdong River, Republic of Korea
    Hyun-Sun Baek, Yong Guan, Min-Ju Kim, Yue Jiang, Mi-Kyung Lee, Ki-Hyun Kim, Jaeyoon Lee, Yuna Shin, Yoon-Ho Kang, Zhun Li
    Antonie van Leeuwenhoek.2023; 116(12): 1317.     CrossRef
  • Identification and genomic analysis of Pseudosulfitobacter koreense sp. nov. isolated from toxin-producing dinoflagellate Alexandrium pacificum
    Yue Jiang, Zhun Li
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum
    Yuxin Peng, Lingmin Jiang, Yue Jiang, Jiyoon Seo, Doeun Jeon, Young-Min Kim, Zhun Li, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Flavobacterium endoglycinae sp. nov., an endophytic bacterium isolated from soybean (Glycine max L. cv. Gwangan) stems
    Jiyoon Seo, Yuxin Peng, Lingmin Jiang, Sang-Beom Lee, Rae-Dong Jeong, Soon Ju Park, Cha Young Kim, Man-Soo Choi, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii
    Yue Jiang, Yuxin Peng, Hyeon Ho Shin, Hyun Jung Kim, Ki-Hyun Kim, Lingmin Jiang, Jiyoung Lee, Zhun Li
    Archives of Microbiology.2022;[Epub]     CrossRef
  • Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum
    Yue Jiang, Lingmin Jiang, Yuxin Peng, Ki-Hyun Kim, Hyeon Ho Shin, Young-Min Kim, Jiyoung Lee, Zhun Li
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila
    Yuxin Peng, Lingmin Jiang, Jiyoon Seo, Zhun Li, Hanna Choe, Jae Cheol Jeong, Suk Weon Kim, Young-Min Kim, Cha Young Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots
    Lingmin Jiang, Myoung Hui Lee, Jae Cheol Jeong, Dae-Hyuk Kim, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil
Inhyup Kim , Jiyoun Kim , Geeta Chhetri , Taegun Seo
J. Microbiol. 2019;57(12):1079-1085.   Published online November 22, 2019
DOI: https://doi.org/10.1007/s12275-019-9350-x
  • 519 View
  • 0 Download
  • 30 Web of Science
  • 33 Crossref
AbstractAbstract PDF
A yellow pigmented, Gram-stain-negative, strictly aerobic, rod-shaped, motile by means of gliding, catalase and oxidase positive bacterium, designated strain DS2-AT, was isolated from soil. Growth was observed at 4–32°C (optimum, 28°C), pH 6–9 (optimum, 7.0), and with 0–0.25% (w/v) NaCl (optimum, 0%). Phylogenetic analysis of 16S rRNA gene sequence revealed that strain DS2-AT belonged to the genus Flavobacterium and was most closely related to Flavobacterium aquatile LMG 4008T (96.4%), Flavobacterium terrae DSM 18829T (95.6%), Flavobacterium vireti THG-SM1T (95.5%), Flavobacterium inkyongense IMCC27201T (95.4%), Flavobacterium brevivitae TTM-43T (95.2%), and Flavobacterium cucumis DSM 18830T (95.2%). Strain DS2-AT produces flexirubin- type pigments. The major fatty acids were iso-C15:0, iso-C17:0 3-OH, and iso-C15:0 3-OH. The major respiratory quinone was identified as menaquinone-6. The major polar lipid was found to be phosphatidylethanolamine. The average nucleotide identity values between strain DS2-AT and selected taxa, F. aquatile LMG 4008T, F. terrae DSM 18829T, and F. cucumis DSM 18830T, were 72, 72.7, and 71.6%, respectively. The draft genome of strain DS2-AT has a number of 14 contigs, scaffold N50 of 476,310 bp and a total size of 3,563,867 bp. Additionally, strain DS2-AT contains 3,127 of gene, 41 of tRNA, 6 of rRNA, and 3 of ncRNA. The DNA G + C content of stain DS2-AT was 40.7 mol%. Based on phylogenetic and phenotypic analyses, strain DS2-AT is considered as a novel species of the genus Flavobacterium, for which the name Flavobacterium humi sp. nov., (type strain DS2-AT = KACC 19715T = JCM 32786T) has been proposed.

Citations

Citations to this article as recorded by  
  • A description of Joostella sp. strain CR20 with potential biotechnological applications
    Muhammad Ramziuddin Zakaria, Maša Vodovnik, Maša Zorec, Kok Jun Liew, Lili Tokiman, Chun Shiong Chong
    Antonie van Leeuwenhoek.2025;[Epub]     CrossRef
  • Paenibacillus suaedae sp. nov. and Paenibacillus violae sp. nov., isolated from the roots of Suaeda japonica Makino and Viola mandshurica W. Becker with plant growth-promoting potential
    Inhyup Kim, Sunho Park, Yonghee Jung, Haejin Woo, Hyunji Lee, Subin Yook, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Pigments from pathogenic bacteria: a comprehensive update on recent advances
    Kusumita Acharya, Swarna Shaw, Sudipta Paul Bhattacharya, Shatarupa Biswas, Suman Bhandary, Arijit Bhattacharya
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • Multiomics dissection of Brassica napus L. lateral roots and endophytes interactions under phosphorus starvation
    Can Liu, Zhen Bai, Yu Luo, Yanfeng Zhang, Yongfeng Wang, Hexin Liu, Meng Luo, Xiaofang Huang, Anle Chen, Lige Ma, Chen Chen, Jinwei Yuan, Ying Xu, Yantao Zhu, Jianxin Mu, Ran An, Cuiling Yang, Hao Chen, Jiajie Chen, Zaifang Li, Xiaodan Li, Yachen Dong, Ji
    Nature Communications.2024;[Epub]     CrossRef
  • Production, characterization and in vitro biological activities of crude pigment from endophytic Micrococcus luteus associated with Avicennia marina
    Gayathri Devi Kandasamy, Preethi Kathirvel
    Archives of Microbiology.2024;[Epub]     CrossRef
  • Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
    Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
    Systematic and Applied Microbiology.2024; 47(4): 126518.     CrossRef
  • Isolation of Massilia species capable of degrading Poly(3-hydroxybutyrate) isolated from eggplant (Solanum melongena L.) field
    Geeta Chhetri, Hyun-Joong Kim, Jong-Min Jeon, Jeong-Jun Yoon
    Chemosphere.2024; 368: 143776.     CrossRef
  • Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment
    Jaincy N. Jayan, Hee-Su Kim, Sathiyaraj Srinivasan, Hyung-Seop Kim, Jae-Yon Yu, Sang-Seob Lee
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant
    Geeta Chhetri, Inhyup Kim, Sunho Park, Yonghee Jung, Taegun Seo
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L.
    Inhyup Kim, Geeta Chhetri, Yoonseop So, Sunho Park, Yonghee Jung, Haejin Woo, Taegun Seo
    Microorganisms.2023; 11(8): 1900.     CrossRef
  • Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter
    Geeta Chhetri, Inhyup Kim, Taegun Seo
    Antonie van Leeuwenhoek.2023; 116(3): 231.     CrossRef
  • A Review of the Chemistry and Biological Activities of Natural Colorants, Dyes, and Pigments: Challenges, and Opportunities for Food, Cosmetics, and Pharmaceutical Application
    Ardalan Pasdaran, Maryam Zare, Azar Hamedi, Azadeh Hamedi
    Chemistry & Biodiversity.2023;[Epub]     CrossRef
  • Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis
    Jina Kim, In-Tae Cha, Ki-Eun Lee, Youn Kyoung Son, Jaewoong Yu, Donghyeok Seol
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil
    Yonghee Jung, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Haejin Woo, Ki-Ho Lee, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Marixanthotalea marina gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater
    Zi-Yue Fu, Hua-Peng Xue, Wei He, Guang-Yuan Ma, Ai Hua Zhang, Dao-Feng Zhang, Wen-Jun Li
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Ideonella oryzae sp. nov., isolated from soil, and Spirosoma liriopis sp. nov., isolated from fruits of Liriope platyphylla
    Yonghee Jung, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Neoroseomonas alba sp. nov., Neoroseomonas nitratireducens sp. nov., Paraoseomonas indoligenes sp. nov and Paraoseomonas baculiformis sp. nov., isolated from the rhizosphere of paddy soil
    Yoonseop So, Geeta Chhetri, Inhyup Kim, Jiyoun Kim, Sunho Park, Yonghee Jung, Taegun Seo
    Antonie van Leeuwenhoek.2023; 116(10): 1009.     CrossRef
  • Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater
    Yoonseop So, Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Byungjo Lee, Wonhee Jang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants
    Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Yoonseop So, Taegun Seo
    Journal of Microbiology.2022; 60(1): 1.     CrossRef
  • An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth
    Geeta Chhetri, Inhyup Kim, Minchung Kang, Yoonseop So, Jiyoun Kim, Taegun Seo
    Microorganisms.2022; 10(6): 1187.     CrossRef
  • Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula)
    Geeta Chhetri, Inhyup Kim, Jiyoun Kim, Yoonseop So, Taegun Seo
    The Journal of Antibiotics.2022; 75(6): 312.     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
  • Fuscibacter oryzae gen. nov., sp. nov., a phosphate-solubilizing bacterium isolated from the rhizosphere of rice plant
    Geeta Chhetri, Minchung Kang, Jiyoun Kim, Inhyup Kim, Yoonseop So, Taegun Seo
    Antonie van Leeuwenhoek.2021; 114(9): 1453.     CrossRef
  • Production, purification, and process optimization of intracellular pigment from novel psychrotolerant Paenibacillus sp. BPW19
    Bhagyashree Padhan, Kasturi Poddar, Debapriya Sarkar, Angana Sarkar
    Biotechnology Reports.2021; 29: e00592.     CrossRef
  • Taibaiella lutea sp. nov., Isolated from Ubiquitous Weedy Grass
    Geeta Chhetri, Inhyup Kim, Jiyoun Kim, Minchung Kang, Taegun Seo
    Current Microbiology.2021; 78(7): 2799.     CrossRef
  • Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula
    Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Yoonseop So, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Characterization of Phosphate Solubilising Bacteria Isolated from Rhizosphere Soils of Piper nigrum L.
    Ashritha ., B. Raghavendr, M. Ramya Rai, P. Nagaraj, P. Visweswara
    Biotechnology(Faisalabad).2021; 20(1): 15.     CrossRef
  • Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island
    Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Minchung Kang, Yoonseop So, Byungjo Lee, Wonhee Jang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant
    Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Byungjo Lee, Wonhee Jang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5382.     CrossRef
  • Reinekea thalattae sp. nov., a New Species of the Genus Reinekea Isolated from Surface Seawater in Sehwa Beach
    Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Minchung Kang, Taegun Seo
    Current Microbiology.2020; 77(12): 4174.     CrossRef
  • Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa
    Lian Xu, Hai-Tao Wang, Jin-Xin Zhang, Hui Zhang, Shuai Wang, Ji-Quan Sun
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(6): 3888.     CrossRef
  • Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater
    Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Minchung Kang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(12): 6180.     CrossRef
  • Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field
    Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Minchung Kang, Byungjo Lee, Wonhee Jang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Anaerotignum faecicola sp. nov., isolated from human faeces
Seung-Hyeon Choi , Ji-Sun Kim , Jam-Eon Park , Keun Chul Lee , Mi Kyung Eom , Byeong Seob Oh , Seung Yeob Yu , Se Won Kang , Kook-Il Han , Min Kuk Suh , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Ju Huck Lee , Jung-Sook Lee , Seung-Hwan Park
J. Microbiol. 2019;57(12):1073-1078.   Published online November 4, 2019
DOI: https://doi.org/10.1007/s12275-019-9268-3
  • 497 View
  • 0 Download
  • 11 Web of Science
  • 11 Crossref
AbstractAbstract PDF
A strictly anaerobic bacterium, designated as strain KGMB- 03357T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10–45°C (optimum temperature of 40°C) and a pH range of 5.1–10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17T (= KCTC 15066T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM 03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3–71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357T are C16:0, C18:0, C18:1 cis 9, and anteiso-C15:0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).

Citations

Citations to this article as recorded by  
  • Dietary supplementation of solubles from shredded, steam-exploded pine particles modulates cecal microbiome composition in broiler chickens
    Chris Major Ncho, Akshat Goel, Vaishali Gupta, Chae-Mi Jeong, Ji-Young Jung, Si-Young Ha, Jae-Kyung Yang, Yang-Ho Choi
    Journal of Animal Science and Technology.2023; 65(5): 971.     CrossRef
  • Cordyceps militaris polysaccharides modulate gut microbiota and improve metabolic disorders in mice with diet‐induced obesity
    Shishi Huang, Yuan Zou, Hongbiao Tang, Jingyu Zhuang, Zhiwei Ye, Tao Wei, Junfang Lin, Qianwang Zheng
    Journal of the Science of Food and Agriculture.2023; 103(4): 1885.     CrossRef
  • Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum
    Nora Köller, Sarah Hahnke, Vladimir Zverlov, Daniel Wibberg, Andreas Klingl, Tobias Busche, Michael Klocke, Alfred Pühler, Andreas Schlüter, Wolfgang Liebl, Irena Maus
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Chakrabartyella piscis gen. nov., sp. nov., a member of the family Lachnospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus
    Bikiran Pardesi, Anthony M. Roberton, Emily M. Wollmuth, Esther R. Angert, Douglas I. Rosendale, William Lindsey White, Kendall D. Clements
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • New Insights into the Physiology of the Propionate Producers Anaerotignum propionicum and Anaerotignum neopropionicum (Formerly Clostridium propionicum and Clostridium neopropionicum)
    Tina Baur, Peter Dürre
    Microorganisms.2023; 11(3): 685.     CrossRef
  • Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021
    Erik Munson, Karen C. Carroll, Romney M. Humphries
    Journal of Clinical Microbiology.2023;[Epub]     CrossRef
  • Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
    Sara Benito-Vaquerizo, Ivette Parera Olm, Thijs de Vroet, Peter J. Schaap, Diana Z. Sousa, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
    Microbial Cell Factories.2022;[Epub]     CrossRef
  • Diarrhea with deficiency kidney-yang syndrome caused by adenine combined with Folium senna was associated with gut mucosal microbiota
    Jiayuan Zhu, Xiaoya Li, Na Deng, Xinxin Peng, Zhoujin Tan
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses
    Irena Maus, Daniel Wibberg, Peter Belmann, Sarah Hahnke, Liren Huang, Cathrin Spröer, Boyke Bunk, Jochen Blom, Alexander Sczyrba, Alfred Pühler, Michael Klocke, Andreas Schlüter
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity
    Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss, Martin J. Blaser
    mBio.2022;[Epub]     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(3): 1443.     CrossRef
Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
Young Joon Oh , Joon Yong Kim , Hyo Kyeong Park , Ja-Young Jang , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
J. Microbiol. 2019;57(11):997-1002.   Published online October 28, 2019
DOI: https://doi.org/10.1007/s12275-019-9421-z
  • 340 View
  • 0 Download
  • 2 Web of Science
  • 3 Crossref
AbstractAbstract PDF
A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium–designated as strain NKC3-5T–was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5–0.7􍾘μm wide and 1.4–2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5–10.0 (optimum pH 9.0), and 25–40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC- 3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2–97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso- C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).

Citations

Citations to this article as recorded by  
  • Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
    Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2021; 59(5): 460.     CrossRef
  • The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
    Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
    Genes.2021; 12(11): 1756.     CrossRef
  • List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Mucilaginibacter limnophilus sp. nov., isolated from a lake
Shih-Yi Sheu , Yi-Ru Xie , Wen-Ming Chen
J. Microbiol. 2019;57(11):967-975.   Published online August 28, 2019
DOI: https://doi.org/10.1007/s12275-019-9146-z
  • 369 View
  • 1 Download
  • 3 Web of Science
  • 4 Crossref
AbstractAbstract PDF
A polyphasic taxonomy approach was used to characterize strain YBJ-36T, isolated from a freshwater lake in Taiwan. Phylogenetic analyses, based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters), indicated that strain YBJ-36T formed a phylogenetic lineage in the genus Mucilaginibacter. 16S rRNA gene sequence similarity indicated that strain YBJ-36T is closely related to species within the genus Mucilaginibacter (93.8–97.8% sequence similarity) and is most similar to Mucilaginibacter fluminis TTM-2T (97.8%), followed by Mucilaginibacter roseus TTM-1T (97.2%). Microbiological analyses demonstrated that strain YBJ-36T is Gram-negative, aerobic, non-motile, rod-shaped, surrounded by a thick capsule, and forms pink-colored colonies. Strain YBJ-36T grew between 20–40°C (optimal range, 35–37°C), pH 5.5–7.0 (optimal pH of 6) and 0–2% NaCl (optimal concentration, 0.5%). The predominant fatty acids of strain YBJ-36T are iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), the major polar lipid is phosphatidylethanolamine, the major polyamine is homospermidine, and the major isoprenoid quinone is MK-7. The draft genome is approximately 4.63 Mb in size with a G+C content of 42.8 mol%. Strain YBJ-36T exhibited less than 35% DNA-DNA relatedness with Mucilaginibacter fluminis TTM-2T and Mucilaginibacter roseus TTM-1T. Based on phenotypic and genotypic properties and phylogenetic inference, strain YBJ-36T should be classified in a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter limnophilus sp. nov. is proposed. The type strain is YBJ-36T (= BCRC 81056T = KCTC 52811T = LMG 30058T).

Citations

Citations to this article as recorded by  
  • Complete genomes of Mucilaginibacter sabulilitoris SNA2 and Mucilaginibacter sp. cycad4: microbes with the potential for plant growth promotion
    Ann M. Hirsch, Ethan Humm, Liudmilla Rubbi, Giorgia Del Vecchio, Sung Min Ha, Matteo Pellegrini, Robert P. Gunsalus, Leighton Pritchard
    Microbiology Resource Announcements.2025;[Epub]     CrossRef
  • Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam
    Ana L. S. Vasconcelos, Fernando Dini Andreote, Thaiane Defalco, Endrews Delbaje, Leticia Barrientos, Armando C. F. Dias, Fabricio Angelo Gabriel, Angelo F. Bernardino, Kattia Núñez-Montero
    Genes.2022; 13(2): 174.     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(3): 1443.     CrossRef
  • Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses
    Lingmin Jiang, Dexin Wang, Ji-Sun Kim, Ju Huck Lee, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3541.     CrossRef
Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain
Lingmin Jiang , Sophea Pheng , Keun Chul Lee , Se Won Kang , Jae Cheol Jeong , Cha Young Kim , Hyeong Cheol Park , Dae-Hyuk Kim , Suk Weon Kim , Song-Gun Kim , Jiyoung Lee
J. Microbiol. 2019;57(11):953-958.   Published online August 28, 2019
DOI: https://doi.org/10.1007/s12275-019-9136-1
  • 328 View
  • 0 Download
  • 12 Web of Science
  • 12 Crossref
AbstractAbstract PDF
A strictly aerobic, motile, endospore-forming, rod-shaped bacterium, designated HS21T, was isolated from rhizospheric soil of the Korean fir tree (Abies koreana) from Halla mountain on Jeju island, Korea. Growth of strain HS21T was observed at pH 6.0–8.0 (optimum: pH 7.0), 0–2% (w/v) NaCl and 4–30°C (optimum: 25°C). A comparative analysis of 16S rRNA gene sequences showed that strain HS21T was most closely related to Cohnella luojiensis HY-22RT (97.6%), followed by C. lupini RLAHU4BT (97.4%) and C. collisoli NKM- 5T (97.2%). The genome of strain HS21T comprised a circular chromosome of 7,059,027 bp with 44.8% G + C content. The DNA-DNA relatedness values between strain HS21T and C. luojiensis HY-22RT and C. lupini RLAHU4BT were 18.1% and 13.8%, respectively. The major cellular fatty acids (> 5%) of the isolate were anteiso-C15:0, iso-C16:0, C16:0, and iso-C15:0. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysylphosphatidylglycerol, and three unidentified aminophospholipids. Based on its phenotypic, phylogenetic, genomic, and chemotaxonomic properties, strain HS21T represents a novel species of the genus Cohnella, for which the name Cohnella abietis sp. nov. is proposed. The type strain is HS21T (= KCTC 43028T = CCTCC AB 2019010T).

Citations

Citations to this article as recorded by  
  • Flavobacterium capsici sp. nov., isolated from the rhizospheric soils of bell pepper (Capsicum annuum L.)
    Dong Hyun Cho, Yuxin Peng, Zalfa Humaira, Yu Lim Park, Hyun Jung Kim, Rae-Dong Jeong, Cha Young Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Description and genomic characterization of Cohnella caldifontis sp. nov., isolated from hot springs in Yunnan province, south-west China
    Ming-Xian Xiang, Cui-Ping Miao, Dian-Yan Zhang, Juan Wang, Yi-Qing Li, Min Yin, ShuKun Tang
    Antonie van Leeuwenhoek.2024;[Epub]     CrossRef
  • Deeply branching Bacillota species exhibit atypical Gram-negative staining
    Jessica K. Choi, Saroj Poudel, Nathan Yee, Jennifer L. Goff, Beile Gao
    Microbiology Spectrum.2024;[Epub]     CrossRef
  • Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir
    Lingmin Jiang, Hanna Choe, Yuxin Peng, Doeun Jeon, Donghyun Cho, Yue Jiang, Ju Huck Lee, Cha Young Kim, Jiyoung Lee
    Journal of Microbiology and Biotechnology.2023; 33(10): 1292.     CrossRef
  • Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil
    Chunling Wang, Lutian Mao, Gegen Bao, Honghui Zhu
    Microorganisms.2023; 11(11): 2726.     CrossRef
  • Flavobacterium litorale sp. nov., isolated from red alga
    Neak Muhammad, Ho Le Han, Yong-Jae Lee, Jaeho Ko, Tra T. H. Nguyen, Song-Gun Kim
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Cohnella herbarum sp. nov., isolated from wild grass fermentation broth
    Miyoung Won, Shin Ae Lee, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster
    Neak Muhammad, Tra T.H. Nguyen, Yong-Jae Lee, Jaeho Ko, Forbes Avila, Song-Gun Kim
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Isolation of Saccharibacillus WB17 strain from wheat bran phyllosphere and genomic insight into the cellulolytic and hemicellulolytic complex of the Saccharibacillus genus
    Ludovic Besaury, Mathilde Bocquart, Caroline Rémond
    Brazilian Journal of Microbiology.2022; 53(4): 1829.     CrossRef
  • Cohnella terricola sp. nov., isolated from soil
    Jiyoun Kim, Geeta Chhetri, Inhyup Kim, Minchung Kang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila
    Yuxin Peng, Lingmin Jiang, Jiyoon Seo, Zhun Li, Hanna Choe, Jae Cheol Jeong, Suk Weon Kim, Young-Min Kim, Cha Young Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Cohnella fermenti sp. nov., isolated from a fermentation process
    Shih-Yao Lin, Wen-Ming Chen, Asif Hameed, Guan-Hua Huang, Mei-Hua Hung, Chiu-Chung Young
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2602.     CrossRef
Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat
In-Tae Cha , Eui-Sang Cho , Yoo Kyung Lee , Seong Woon Roh , Myung-Ji Seo
J. Microbiol. 2019;57(7):569-574.   Published online June 27, 2019
DOI: https://doi.org/10.1007/s12275-019-8666-x
  • 364 View
  • 0 Download
  • 4 Web of Science
  • 4 Crossref
AbstractAbstract PDF
Strain ML311-T8T was isolated from a glacial retreat area in Svalbard, Norway, and was taxonomically characterized by a polyphasic approach. Upon phylogenetic analysis, strain ML311-T8T was clustered with Paenibacillus arcticus MME2_ R6T and P. contaminans CKOBP-6T with 98.3–98.6 and 93.5– 93.9% 16S rRNA gene sequence similarities, respectively. DNA-DNA hybridization values between strain ML311-T8T and P. arcticus MME2_R6T was 19.9%. The genomic DNA G+C content was 41.1 mol%. The isolated strain was Gramstain- positive, strictly aerobic and rod-shaped, and grew in 0–0.5% (w/v) NaCl, at 4–23°C and pH 6.0–10.0, with optimal growth in 0% (w/v) NaCl, at 20°C and pH 7.0–8.0. The predominant respiratory quinone of strain ML311-T8T was MK- 7 and the major fatty acids were anteiso-C15:0 and C16:0. The polar lipids of strain ML311-T8T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified amino lipids, and three unidentified lipids. On the basis of polyphasic taxonomic analysis, the strain ML311-T8T is proposed to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus psychroresistens sp. nov. is proposed. The type strain is ML311-T8T (= KCCM 43190T = JCM 31243T).

Citations

Citations to this article as recorded by  
  • Microbiodiversity Landscape Present in the Mine-Tailings of the “Sierra de Huautla” Biosphere Reserve, Mexico
    Maikel Gilberto Fernández-López, Ayixon Sánchez-Reyes, Marcos Eduardo Rosas-Ramírez, Edgar Balcázar-López
    Water, Air, & Soil Pollution.2024;[Epub]     CrossRef
  • Paenibacillus dendrobii sp. nov., an indole-3-acetic acid-producing endophytic bacterium isolated from Dendrobium nobile
    Yadong Hu, Hongjie Li, Yaoyi Chen, Qiling Zhang, Shigang Zheng, Dan Rao, Ze Chun, Ruoxi Zhao
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Validation List no. 206. 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 .2022;[Epub]     CrossRef
  • Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil
    Jayoung Paek, Lu Bai, Yeseul Shin, Hongik Kim, Joong-Ki Kook, Young-Hyo Chang
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp
Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee
J. Microbiol. 2019;57(6):444-449.   Published online May 27, 2019
DOI: https://doi.org/10.1007/s12275-019-8704-8
  • 351 View
  • 0 Download
  • 6 Web of Science
  • 6 Crossref
AbstractAbstract PDF
A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA- 4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0 (optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl (optimum, 0–2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA- 4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).

Citations

Citations to this article as recorded by  
  • Bacteroides faecium sp. nov. isolated from human faeces
    Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young-Do Nam, Yoon-E Choi, Seong Woon Roh
    International Journal of Systematic and Evolutionary Microbiology.2023;[Epub]     CrossRef
  • ODFM, an omics data resource from microorganisms associated with fermented foods
    Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
    Scientific Data.2021;[Epub]     CrossRef
  • Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana
    Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Jin-Woo Bae
    International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5439.     CrossRef
  • Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa
    Anusha Rai, Smita N, Suresh G, Shabbir A, Deepshikha G, Sasikala Ch, Ramana Ch.V
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1720.     CrossRef
  • Pectin Degradation is an Important Determinant for Alfalfa Silage Fermentation through the Rescheduling of the Bacterial Community
    Bing Wang, Zhiqiang Sun, Zhu Yu
    Microorganisms.2020; 8(4): 488.     CrossRef
  • Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana
    Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Jin-Woo Bae
    International Journal of Systematic and Evolutionary Microbiology.2019; 69(9): 2948.     CrossRef
Edaphovirga cremea gen. nov., sp. nov., isolated from the rhizospheric soil of Codonopsis clematidea
Jin-Yan Xue , Meng-Yue Zhang , Yu Zhang , Juan Cheng , Li-Cheng Liu , Ying-Ying Wu , Tian-Yuan Zhang , Yi-Xuan Zhang
J. Microbiol. 2019;57(5):337-342.   Published online February 26, 2019
DOI: https://doi.org/10.1007/s12275-019-8408-0
  • 329 View
  • 0 Download
  • 1 Crossref
AbstractAbstract PDF
A Gram-negative, facultatively anaerobic, non-motile, nonspore- forming, coccoid or rod-shaped and creamy-pigmented bacterium, designated SYP-B2100T, was isolated from the rhizospheric soil of Codonopsis clematidea in the Xinjiang Uygur Autonomous Region, China. The optimal growth occurred at 28°C, pH 5.0, in the absence of NaCl. The cells tested positive in catalase and methyl red tests but negative in oxidase, urease, gelatinase, milk coagulation, and peptonisation, H2S production, nitrate reduction, and Voges-Proskauer tests. The major isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were C16:0 and summed feature 8. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The 16S rRNA gene sequence of strain SYP-B2100T was the most similar to that of Rahnella inusitata DSM 30078T (96.9%) within the family Enterobacteriaceae. The genomic DNA G+C content of strain SYP-B2100T was 50.3 mol%. The combined data from the phylogenetic, morphological, physiological, biochemical, and chemotaxonomic analyses presented in this study support the conclusion that strain SYP-B2100T represents a novel species of a new genus, for which the name Edaphovirga cremea gen. nov., sp. nov. is proposed; the type strain is SYPB2100T (= CGMCC 1.5857T = DSM 105170T = KCTC 62024T).

Citations

Citations to this article as recorded by  
  • Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
    Lingmin Jiang, Dexin Wang, Jung-Sook Lee, Dae-Hyuk Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    Journal of Microbiology.2020; 58(5): 357.     CrossRef
Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River
Yochan Joung , Hye-Jin Jang , Jaeho Song , Jang-Cheon Cho
J. Microbiol. 2019;57(5):343-349.   Published online February 5, 2019
DOI: https://doi.org/10.1007/s12275-019-8436-9
  • 324 View
  • 0 Download
  • 10 Web of Science
  • 11 Crossref
AbstractAbstract PDF
A non-motile, yellow-pigmented bacterial strain, designated IMCC34762T, was isolated from a freshwater sample collected from Lake Cheongpyeong in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC- 34762T formed a lineage within the genus Flavobacterium and was most closely related to F. pectinovorum DSM 6368T (98.3% sequence similarity), followed by F. piscis CCUG 60099T (98.3%), F. branchiicola 59B-3-09T (98.2%), and F. saccharophilum DSM 1811T (98.2%). The average nucleotide identity and the genome-to-genome distance between strain IMCC34762T and the closely related strains were 61–62% and 26–27%, respectively, indicating that IMCC34762T is a novel species of the genus Flavobacterium. The major fatty acids (> 5%) of strain IMCC34762T were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c, 17.3%), iso-C15:0 (15.0%), iso-C15:0 G (9.0%), C15:0 ω6c (7.4%), iso-C15:0 (7.4%), and iso-C16:0 (5.3%). The major respiratory quinone and polyamine were MK-6 and sym-homospermidine, respectively. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and an unidentified lipid. The DNA G+C content of strain IMCC34762T was 34.4 mol%. Based on the taxonomic data presented in this study, strain IMCC34762T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium aquariorum, sp. nov. is proposed. The type strain is IMCC34762T (= KACC 19725T = NBRC 113425T).

Citations

Citations to this article as recorded by  
  • Flavobacterium algoriphilum sp. nov., Flavobacterium arabinosi sp. nov., Flavobacterium cryoconiti sp. nov., Flavobacterium galactosi sp. nov., Flavobacterium melibiosi sp. nov., and Flavobacterium algoris sp. nov., six novel cold-adapted bacteria isolate
    Lei-Lei Yang, Yu-Hua Xin, Qing Liu
    BMC Microbiology.2025;[Epub]     CrossRef
  • Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea
    Jung-Hun Jo, Soon-Youl Lee, Se-Yoon Chun, Wan-Taek Im
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
  • Unveiling the hidden threat: heavy metal accumulation in crops and soil microbial dynamics in a teaching experimental farmland
    Xue Gu, Xuegang Yu, Qing Li, Yanjun Mao, Zhiwei Zhou, Huan Hu, Rui Huang, Jiayu Zhou, Yuanyi Sun, Yancheng Li, Aijiang Yang
    Plant and Soil.2025;[Epub]     CrossRef
  • Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
    Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
    Journal of Microbiology.2023; 61(5): 495.     CrossRef
  • Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
    Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
    Journal of Microbiology.2022; 60(9): 890.     CrossRef
  • Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont
    Izzet Burcin Saticioglu
    Archives of Microbiology.2021; 203(9): 5783.     CrossRef
  • Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout
    Muhammed Duman, Hilal Ay, Soner Altun, Nevzat Sahin, Izzet Burcin Saticioglu
    International Journal of Systematic and Evolutionary Microbiology.2021;[Epub]     CrossRef
  • Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey
    Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Muhammed Duman, Nevzat Sahin
    Systematic and Applied Microbiology.2021; 44(2): 126186.     CrossRef
  • Flavobacterium bernardetii sp. nov., a possible emerging pathogen of farmed rainbow trout (Oncorhynchus mykiss) in cold water
    Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nevzat Sahin, Muhammed Duman
    Aquaculture.2021; 540: 736717.     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
  • 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
Chryseolinea soli sp. nov., isolated from soil
Shin Ae Lee , Yiseul Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon
J. Microbiol. 2019;57(2):122-126.   Published online January 31, 2019
DOI: https://doi.org/10.1007/s12275-019-8562-4
  • 407 View
  • 0 Download
  • 19 Web of Science
  • 19 Crossref
AbstractAbstract PDF
A yellow-colored bacterium with gliding motility, strain KIS68-18T, was isolated from a soil sample at Bijin Island in Tongyeong city, Republic of Korea. The cells were strictly aerobic, Gram-staining-negative, non-spore-forming, and rod-shaped. The strain grew at the range of 10–35°C (optimum, 25–30°C), pH 5.5–8.0 (optimum, 6.0–7.5), and 0–0.5% (w/v) NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KIS68-18T was closely related to Chryseolinea serpens DSM 24574T (98.9%) and had low sequence similarities (below 92.6%) with other members of the family ‘Cytophagaceae’ in the phylum Bacteroidetes. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were C16:1 ω5c (38.8%), iso-C15:0 (18.5%), and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c, 10.6%). The polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid, three unidentified aminophospholipids, two unidentified aminolipids, and five unidentified lipids. The DNA G + C content was 50.9%. Based on the phylogenetic, physiological, and chemotaxonomic data, stain KIS68-18T represents a novel species of the genus Chryseolinea, for which the name Chryseolinea soli sp. nov. is proposed. The type strain of Chryseolinea soli is KIS68-18T (= KACC 17327T = NBRC 113100T).

Citations

Citations to this article as recorded by  
  • Rhizosphere bacteriome assemblage following initial fluctuations is delayed with nitrogen additions in tomato seedlings
    Mary M. Dixon, Carley R. Rohrbaugh, Daniel K. Manter, Jorge A. Delgado, Jorge M. Vivanco
    Biology and Fertility of Soils.2025; 61(2): 233.     CrossRef
  • Assessment of temperature dynamics during methane oxidation in a pilot scale compost biofilter
    Tania L. Gómez-Borraz, Yuly Vanessa Torres-Arévalo, Yovany Cuetero-Martínez, Armando González-Sánchez, Adalberto Noyola
    Bioresource Technology.2025; 419: 132097.     CrossRef
  • Microbiome re-assembly enhances manganese and ammonium co-removal in sand biofilters
    Xin Zhao, Xuan Zhou, Bo Sun, Chuanjun Dai, Qing Guo, Dezhao Liu, Xiangyong Zheng, Min Zhao
    Separation and Purification Technology.2025; 369: 132902.     CrossRef
  • Solid vermicompost and its liquid derivative exhibit strong biocontrol properties against Myzus persicae aphids on sweet pepper
    Mey Jerbi-Elayed, Stefan Brandl, Grégory Sempo, John Riviere, Deborah Lanterbecq, Marie Annet, Leidy Grawez Demoulin, Muriel Quinet, Stanley Lutts, Thierry Hance, François Renoz
    Journal of Pest Science.2025;[Epub]     CrossRef
  • Poultry litter biochar soil amendment affects microbial community structures, promotes phosphorus cycling and growth of barley (Hordeum vulgare)
    Lea Deinert, Shakhawat Hossen, Israel Ikoyi, Witold Kwapinksi, Matthias Noll, Achim Schmalenberger
    European Journal of Soil Biology.2024; 120: 103591.     CrossRef
  • Uptake and Metabolic Conversion of Exogenous Phosphatidylcholines Depending on Their Acyl Chain Structure in Arabidopsis thaliana
    Ekaterina R. Kotlova, Svetlana V. Senik, Gregory A. Pozhvanov, Ilya A. Prokopiev, Ivan A. Boldyrev, Bairta S. Manzhieva, Ekaterina Ya. Amigud, Roman K. Puzanskiy, Anna A. Khakulova, Evgeny B. Serebryakov
    International Journal of Molecular Sciences.2023; 25(1): 89.     CrossRef
  • A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species
    Lingmin Jiang, Jiyoon Seo, Yuxin Peng, Doeun Jeon, Ju Huck Lee, Cha Young Kim, Jiyoung Lee
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation
    Fadime Ozdemir Kocak, Saadet Gizem Ertekin Tanir, Ayten Kumas Cetin, Levent Degirmenci
    World Journal of Microbiology and Biotechnology.2023;[Epub]     CrossRef
  • Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir
    Lingmin Jiang, Hanna Choe, Yuxin Peng, Doeun Jeon, Donghyun Cho, Yue Jiang, Ju Huck Lee, Cha Young Kim, Jiyoung Lee
    Journal of Microbiology and Biotechnology.2023; 33(10): 1292.     CrossRef
  • The Effect of Long-Term Agricultural Use on the Bacterial Microbiota of Chernozems of the Forest-Steppe Zone
    Konstantin S. Boyarshin, Valeria V. Adamova, Zheng Wentao, Olga Y. Obuhova, Marina V. Kolkova, Vitaliy A. Nesterenko, Olga S. Bespalova, Violetta V. Kluyeva, Kristina A. Degtyareva, Yulia N. Kurkina, Olesia A. Makanina, Irina V. Batlutskaya
    Diversity.2023; 15(2): 191.     CrossRef
  • Chryseolinea lacunae sp. nov. and Piscinibacter lacus sp. nov. Isolated from Artificial Pond Water
    Inhyup Kim, Geeta Chhetri, Jiyoun Kim, Yoonseop So, Taegun Seo
    Current Microbiology.2023;[Epub]     CrossRef
  • Impact of sheep wool residues as soil amendments on olive beneficial symbionts and bacterial diversity
    Michela Palla, Alessandra Turrini, Caterina Cristani, Laura Bonora, David Pellegrini, Jacopo Primicerio, Arianna Grassi, Filip Hilaj, Manuela Giovannetti, Monica Agnolucci
    Bioresources and Bioprocessing.2022;[Epub]     CrossRef
  • Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov.
    Chunling Wang, Yingying Lv, Anzhang Li, Qing Yao, Honghui Zhu
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Draft Genome Sequence of Cytophagales sp. Strain WSM2-2, Isolated from Garden Soil
    Masataka Aoki, Mamoru Oshiki, Mizuki Iwagaki, Masashi Hatamoto, Takashi Yamaguchi, Nobuo Araki, J. Cameron Thrash
    Microbiology Resource Announcements.2021;[Epub]     CrossRef
  • Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse
    Yang Li, Jingliang Chi, Jing Ao, Xiaomei Gao, Xiaohui Liu, Yulu Sun, Weiwei Zhu
    Current Microbiology.2021; 78(6): 2380.     CrossRef
  • Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape (Vitis vinifera L.)
    Lingmin Jiang, Doeun Jeon, Jueun Kim, Chul Won Lee, Yuxin Peng, Jiyoon Seo, Ju Huck Lee, Jin Hyub Paik, Cha Young Kim, Jiyoung Lee
    Frontiers in Microbiology.2021;[Epub]     CrossRef
  • Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
    Lingmin Jiang, Chan Ju Lim, Song-Gun Kim, Jae Cheol Jeong, Cha Young Kim, Dae-Hyuk Kim, Suk Weon Kim, Jiyoung Lee
    Journal of Microbiology.2020; 58(1): 24.     CrossRef
  • Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
    Lingmin Jiang, Dexin Wang, Jung-Sook Lee, Dae-Hyuk Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    Journal of Microbiology.2020; 58(5): 357.     CrossRef
  • Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots
    Lingmin Jiang, Myoung Hui Lee, Jae Cheol Jeong, Dae-Hyuk Kim, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond
Tingye Feng , Sang Eun Jeong , Jin Ju Lim , Seogang Hyun , Che Ok Jeon
J. Microbiol. 2019;57(4):232-237.   Published online January 16, 2019
DOI: https://doi.org/10.1007/s12275-019-8463-6
  • 331 View
  • 0 Download
  • 6 Web of Science
  • 6 Crossref
AbstractAbstract PDF
A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27T was observed at 20–40°C (optimum, 30°C), pH 5.0–7.0 (optimum, pH 6.0), and 0–0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C16:0, cyclo-C17:0, and cyclo- C19:0 ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27T was most closely related to Paraburkholderia rhynchosiae WSM3937T, Paraburkholderia ginsengiterrae DCY85T, Paraburkholderia fungorum NBRC 102489T, and Paraburkholderia graminis C4D1MT with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27T (KACC 19714 T = JCM 32721T).

Citations

Citations to this article as recorded by  
  • International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021
    Seyed Abdollah Mousavi, J. Peter W. Young
    International Journal of Systematic and Evolutionary Microbiology.2022;[Epub]     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
  • The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species
    Chrizelle W. Beukes, Stephanus N. Venter, Emma T. Steenkamp
    Grass and Forage Science.2021; 76(1): 10.     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
  • Flavihumibacter soli sp. nov., Isolated from Soil
    Ye Lin Seo, Jaejoon Jung, Shehzad Abid Khan, Kyung Hyun Kim, Che Ok Jeon
    Current Microbiology.2020; 77(10): 3179.     CrossRef
  • List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Flavisolibacter aluminii sp. nov., a novel member of the genus Flavisolibacter isolated from an automotive air conditioning system
Hyosun Lee , Dong-Uk Kim , Suyeon Lee , Song-Gun Kim , A-Young Park , Jae-Hyung Ahn , Jong-Ok Ka
J. Microbiol. 2019;57(1):18-22.   Published online November 19, 2018
DOI: https://doi.org/10.1007/s12275-019-8219-3
  • 309 View
  • 0 Download
  • 3 Web of Science
  • 2 Crossref
AbstractAbstract PDF
A Gram-stain-negative, aerobic, non-motile, rod-shaped, and yellow-pigmented bacterium, designated strain ID1709T, was isolated from an automotive air conditioning system collected in Korea. Analysis of 16S rRNA gene sequence similarity showed that strain ID1709T had 92.2–94.3% similarities with the type strains of members of the genus Flavisolibacter. The major cellular fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant respiratory quinone was MK-7. The polar lipids comprised phosphatidylethanolamine, aminoglycophospholipid, two unidentified aminolipids, and three unidentified lipids. The DNA G + C content of the strain was 35.6 mol%. Based on phenotypic, chemotaxonomic, and genotypic data, strain ID1709T represents a novel species in the genus Flavisolibacter, for which the name Flavisolibacter aluminii sp. nov. (= KACC 19451T = KCTC 52778T = NBRC 112870T), is proposed.

Citations

Citations to this article as recorded by  
  • Insights into the Response and Evolution of Microbial Communities During Long-Term Natural Remediation of Contaminated Abandoned Shale Gas Wells
    Hongyang Ren, Shuangli Chen, Jiajian Shang, Yujia Gao, Yuanpeng Deng, Zhaoyang Wang, Guojun Hu, Bing Wang
    Water, Air, & Soil Pollution.2024;[Epub]     CrossRef
  • Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system
    Jong Sung Lim, Hyosun Lee, Jigwan Son, Song-Gun Kim, Dong-Uk Kim, Jong-Ok Ka
    Archives of Microbiology.2021; 203(7): 4073.     CrossRef
Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
Ja-Young Jang , Young Joon Oh , Seul Ki Lim , Hyo Kyeong Park , Changsu Lee , Joon Yong Kim , Mi-Ai Lee , Hak-Jong Choi
J. Microbiol. 2018;56(12):880-885.   Published online October 25, 2018
DOI: https://doi.org/10.1007/s12275-018-8518-0
  • 392 View
  • 0 Download
  • 11 Web of Science
  • 12 Crossref
AbstractAbstract PDF
A moderately halophilic and alkalitolerant bacterial strain NKC1-1T was isolated from commercial kimchi in Korea. Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0–25% (w/v) NaCl (optimal at 10% [w/v]), at 20–40°C (optimal at 37°C) and pH 6.5–10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7–92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537T; KCCM 43276T).

Citations

Citations to this article as recorded by  
  • A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families
    Yangjie Li, Dechao Zhang, Dexin Bo, Donghai Peng, Ming Sun, Jinshui Zheng
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives
    Sharareh Harirchi, Taner Sar, Mohaddaseh Ramezani, Habibu Aliyu, Zahra Etemadifar, Seyed Ali Nojoumi, Fatemeh Yazdian, Mukesh Kumar Awasthi, Mohammad J. Taherzadeh
    Microorganisms.2022; 10(12): 2355.     CrossRef
  • Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
    Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2021; 59(5): 460.     CrossRef
  • The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
    Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
    Genes.2021; 12(11): 1756.     CrossRef
  • Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection
    Seung Woo Ahn, Se Hee Lee, Uh Jin Kim, Hee-Chang Jang, Hak-Jong Choi, Hyon E. Choy, Seung Ji Kang, Seong Woon Roh
    Gut Pathogens.2021;[Epub]     CrossRef
  • Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar salt
    Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Se Hee Lee, Na-Ri Shin, Jin-Woo Bae, Jinjong Myoung, Ki-Eun Lee, In-Tae Cha, Jin-Kyu Rhee, Seong Woon Roh
    Systematic and Applied Microbiology.2020; 43(3): 126085.     CrossRef
  • Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses
    Min Young Jung, Changsu Lee, Myung-Ji Seo, Seong Woon Roh, Se Hee Lee
    BMC Microbiology.2020;[Epub]     CrossRef
  • Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food
    Young Joon Oh, Joon Yong Kim, Hee Eun Jo, Hyo Kyeong Park, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2020; 58(5): 387.     CrossRef
  • Effects of an auxin-producing symbiotic bacterium on cell growth of the microalga Haematococcus pluvialis: Elevation of cell density and prolongation of exponential stage
    Changsu Lee, Min Seo Jeon, Joon Yong Kim, Se Hee Lee, Dae Geun Kim, Seong Woon Roh, Yoon-E Choi
    Algal Research.2019; 41: 101547.     CrossRef
  • Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
    Young Joon Oh, Joon Yong Kim, Hyo Kyeong Park, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2019; 57(11): 997.     CrossRef
  • List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
  • Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying
    Floriane Gaucher, Koffigan Kponouglo, Houem Rabah, Sylvie Bonnassie, Jordane Ossemond, Sandrine Pottier, Julien Jardin, Valérie Briard-Bion, Pierre Marchand, Philippe Blanc, Romain Jeantet, Gwénaël Jan
    Frontiers in Microbiology.2019;[Epub]     CrossRef
Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea
Eui-Sang Cho , In-Tae Cha , Hak-Jong Choi , Seong Woon Roh , Young-Do Nam , Sung Man Seo , Myung-Ji Seo
J. Microbiol. 2018;56(12):868-873.   Published online October 25, 2018
DOI: https://doi.org/10.1007/s12275-018-8231-z
  • 316 View
  • 0 Download
  • 6 Web of Science
  • 6 Crossref
AbstractAbstract PDF
A yellow pigmented bacterium designated strain MBLN094T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16T, Z. profunda SM-A87T, Z. atlantica 22II14-10F7T, and Z. endophytica CPA58T, respectively. Strain MBLN094T grew at 20‒37°C (optimum, 25‒ 30°C), at pH 6.0‒10.0 (optimum, 7.0‒8.0), and with 0.5‒15.0% (w/v) NaCl (optimum, 2.0‒5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C17:0 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094T (= KCTC 62279T = JCM 32262T).

Citations

Citations to this article as recorded by  
  • 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
  • Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
    Yu-Yan Yue, Yu-Qi Ye, Zi-Yang Zhou, Meng-Di Zhang, Ya-Wei Jia, Zong-Jun Du
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Validation List no. 206. 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 .2022;[Epub]     CrossRef
  • Zunongwangia pacifica sp. nov., isolated from surface seawater of the Western Pacific Ocean
    Yongqing Chen, Tianqi Liu, Qiliang Lai, Chunming Dong, Zongze Shao
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory
    Lingmin Jiang, Dexin Wang, Jung-Sook Lee, Dae-Hyuk Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    Journal of Microbiology.2020; 58(5): 357.     CrossRef
  • Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta
    Jaeho Song, Yeonjung Lim, Hye-Jin Jang, Yochan Joung, Ilnam Kang, Seong-Joo Hong, Choul-Gyun Lee, Jang-Cheon Cho
    Journal of Microbiology.2019; 57(11): 982.     CrossRef
Roseovarius tibetensis sp. nov., a halophilic bacterium isolated from Lake LongmuCo on Tibetan Plateau
Hui-bin Lu , Xiao-feng Xue , Dorji Phurbu , Peng Xing , Qing-long Wu
J. Microbiol. 2018;56(11):783-789.   Published online October 24, 2018
DOI: https://doi.org/10.1007/s12275-018-8178-0
  • 371 View
  • 0 Download
  • 7 Crossref
AbstractAbstract PDF
Two Gram-stain negative halophilic strains, designated as LM2T and LM4, were isolated from Lake LongmuCo on Tibetan Plateau. These two strains were aerobic, catalaseand oxidase- positive, nonmotile and rod-shaped organisms. Phylogenetic analysis based on 16S rRNA gene sequences indicated that LM2T and LM4 belong to the genus Roseovarius, with Roseovarius tolerans EL-172T (97.3% and 97.4% 16S rRNA gene sequence similarity, respectively) and Roseovarius azorensis SSW084T (95.5% and 95.6% 16S rRNA gene sequence similarity, respectively) as their closest neighbors. Q-10 was the sole respiratory quinone of these two strains. The major fatty acids were C18:1 ω7c/C18:1 ω6c, C16:0, C19:0 cyclo ω8c, and 11-methyl C18:1 ω7c. The polar lipids included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phospholipid of unknown structure containing glucosamine, and unidentified aminolipid. The DNA G + C content was between 64.2 and 64.5 mol%. DNA-DNA hybridization showed 96.7% relatedness between LM2T and LM4, 24.9% relatedness between LM2T and R. tolerans EL-172T, and 36.3% relatedness between LM4 and R. tolerans EL-172T. Based on phylogenetic analysis, DNA-DNA hybridization, a range of physiological and biochemical characteristics, LM2T and LM4 belong to the same species and were clearly distinguished from the type strains of the genus Roseovarius. It was evident that LM2T and LM4 could be classified as a novel species of the genus Roseovarius, for which the name Roseovarius tibetensis sp. nov. is proposed. The type strain is LM2T (= CGMCC 1.16230T = KCTC 62028T).

Citations

Citations to this article as recorded by  
  • Nioella halotolerans sp. nov., a novel member of the family Roseobacteraceae, isolated from a saline lake
    Shuai-Bo Han, Xin-Jun Hou, Yu Li, Xiao-Long He, Rui-Jun Wang, Xu-Fen Zhu, Min Wu
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
  • Lithoautotrophic lifestyle of the widespread genusRoseovariusrevealed by physiological and genomic characterization ofRoseovarius autotrophicussp. nov
    Galina Slobodkina, Nataliya Ratnikova, Alexander Merkel, Vadim Kevbrin, Alexandra Kuchierskaya, Alexander Slobodkin
    FEMS Microbiology Ecology.2022;[Epub]     CrossRef
  • Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella
    Hui-Bin Lu, Zhi-Peng Cai, Yong-Gang Yang, Mei-Ying Xu
    Antonie van Leeuwenhoek.2020; 113(8): 1155.     CrossRef
  • Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China
    Hui-Bin Lu, Tong-Chu Deng, Mei-Ying Xu
    Current Microbiology.2020; 77(10): 3185.     CrossRef
  • Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau
    Peixin Gao, Huibin Lu, Peng Xing, Qinglong L. Wu
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5217.     CrossRef
  • Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge
    Lingping Zhuang, Lianzhong Luo
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(1): 274.     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(3): 597.     CrossRef
Aestuariibaculum marinum sp. nov., a marine bacterium isolated from seawater in South Korea
Jiwon Choi , Dongwook Lee , Jun Hyeong Jang , Seho Cha , Taegun Seo
J. Microbiol. 2018;56(9):614-618.   Published online August 23, 2018
DOI: https://doi.org/10.1007/s12275-018-8134-z
  • 350 View
  • 0 Download
  • 10 Crossref
AbstractAbstract PDF
A Gram-negative, non-motile, aerobic bacterium, designated strain IP7T, was isolated from seawater at the shore of the Incheon Eulwang-ri beach, South Korea. Cells of strain IP7T are straight or slightly rod-shaped and colonies are round, convex and orange-yellow. Strain IP7T is flexirubin-negative, mild halophile, catalase- and oxidase-positive, and produces a yellow-orange carotenoid pigment. Growth is optimal at 30°C, pH 7–9, and 2.0–4.0% NaCl (w/v). On the basis of 16S rRNA gene sequence similarity, strain IP7T is affiliated with genus Aestuariibaculum in the family Flavobacteriaceae, the closest relative being Aestuariibaculum suncheonense SC17T (98.3% sequence similarity). The DNA G + C content of the novel strain is 37.4 mol%. The only quinone is MK-6 menaquinone. Iso-branched C15:0, iso-branched C15:1 G, and iso-branched C17:0 3-OH are major fatty acids. The major polar lipids are phosphatidylethanolamine, an unidentified aminoglycolipid and two unidentified glycolipids. The DNA-DNA hybridization value of strain IP7T with Aestuariibaculum suncheonense SC17T is 28.87%. Based on the collective DNA-DNA hybridization, biochemical, phylogenetic and physiological data, we report a novel species of the genus Aestuariibaculum for which the name Aestuariibaculum marinum sp. nov. is proposed. The type strain is IP7T (= KCTC 52521T = JCM 31725T).

Citations

Citations to this article as recorded by  
  • Marixanthotalea marina gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater
    Zi-Yue Fu, Hua-Peng Xue, Wei He, Guang-Yuan Ma, Ai Hua Zhang, Dao-Feng Zhang, Wen-Jun Li
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Complete genome sequence of carotenoid-producing Aestuariibaculum lutulentum L182T isolated from the tidal sediment
    Wen-Jia Liu, Jia-Wei Gao, Yu Zhang, Cong Sun, Lin Xu
    Marine Genomics.2023; 72: 101074.     CrossRef
  • Aestuariibaculum lutulentum sp. nov., a marine bacterium isolated from coastal sediment in Beihai
    Jia-Wei Gao, Dong-Yan He, Wen-Wu Zhang, Yu-Ruo Wang, Yue Su, Jun-Jie Ying, Zhi-Cheng Wu, Wu Qu, Lin Xu, Cong Sun
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Aestuariibaculum sediminum sp. nov., a marine bacterium isolated from a tidal flat in Zhoushan
    Zhi-Cheng Wu, Xin-Yin Zhang, Cong Sun, Lin Xu, Ge-Yi Fu, Xue-Wei Xu
    Archives of Microbiology.2021; 203(6): 2953.     CrossRef
  • The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
    Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
    Genes.2021; 12(11): 1756.     CrossRef
  • Snuella sedimenti sp. nov., isolated from marine sediment
    Jong-Hwa Kim, Veeraya Weerawongwiwat, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, Wonyong Kim
    Archives of Microbiology.2021; 203(9): 5437.     CrossRef
  • Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant
    Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Byungjo Lee, Wonhee Jang, Taegun Seo
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5382.     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(1): 5.     CrossRef
  • Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil
    Inhyup Kim, Jiyoun Kim, Geeta Chhetri, Taegun Seo
    Journal of Microbiology.2019; 57(12): 1079.     CrossRef
  • Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond
    Tingye Feng, Sang Eun Jeong, Jin Ju Lim, Seogang Hyun, Che Ok Jeon
    Journal of Microbiology.2019; 57(4): 232.     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
  • 329 View
  • 1 Download
  • 7 Crossref
AbstractAbstract 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
Leifsonia flava sp. nov., a novel actinobacterium isolated from the rhizosphere of Aquilegia viridiflora
Ying Cai , Wen-Zhen Tao , Yu-Jun Ma , Juan Cheng , Meng-Yue Zhang , Yi-Xuan Zhang
J. Microbiol. 2018;56(8):549-555.   Published online July 25, 2018
DOI: https://doi.org/10.1007/s12275-018-8061-z
  • 365 View
  • 0 Download
  • 9 Crossref
AbstractAbstract PDF
SYP-B2174T is a yellow-pigmented, Gram-positive, non-motile, and rod-shaped actinobacterium isolated from the rhizospheric soil of Aquilegia viridiflora Pall. collected from the Xinjiang uygur autonomous region of China. The strain’s growth temperature ranges from 1 to 35°C, with an optimal growth being observed at 28°C. Growth occurs from 0 to 5% NaCl and at pH 6–8, with optimal growth being observed in 1% NaCl at pH 7. Comparative 16S rRNA gene sequencebased phylogenetic analysis placed the strain in a clade with the species Leifsonia kafniensis JCM 17021T and Leifsonia psychrotolerans DSM 22824T with similarities of 97.8 and 97.6%, respectively. The DNA-DNA hybridization values of the strain SYP-B2174T to its closest phylogenetic neighbors were significantly lower than 35.7%. The strain was identified as a novel species of the genus Leifsonia judging by the coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, principal phospholipids phosphatidylglycerol and diphosphatidylglycerol, major menaquinone MK-11, predominant fatty acids of anteiso-C15:0, anteiso-C17:0, and iso-C16:0, and a DNA G + C base composition of 68.7 mol%, for which the name Leifsonia flava sp. nov. is proposed. The type strain is SYP-B2174T (= CGMCC 1.15856T = DSM 105144T = KCTC 39963T).

Citations

Citations to this article as recorded by  
  • Leifsonia stereocauli sp. nov., Isolated from Stereocaulon tomentosum Fr. Lichen
    Shu-Ya Zuo, Lian-Shuang Xiong, Qing Yuan, Guo-Hua Chen, Rui Yang, Li-Song Wang, Cheng-Lin Jiang, Xin-Yu Wang, Yi Jiang
    Current 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
  • Validation list no. 225: 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
  • Enhancement of the germination and growth of Panicum miliaceum and Brassica juncea in Cd- and Zn-contaminated soil inoculated with heavy-metal-tolerant Leifsonia sp. ZP3
    Ian Cho, Soo Yeon Lee, Kyung-Suk Cho
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • Plant Growth-Promoting and Tequila Vinasse-Resistant Bacterial Strains
    Alberto J. Valencia-Botín, Ismael F. Chávez-Díaz, Florentina Zurita-Martínez, Allan Tejeda-Ortega, Lily X. Zelaya-Molina
    Microbiology Research.2024; 15(3): 1144.     CrossRef
  • Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes
    Anna C. Simpson, Pratyay Sengupta, Flora Zhang, Asif Hameed, Ceth W. Parker, Nitin K. Singh, Georgios Miliotis, Punchappady D. Rekha, Karthik Raman, Christopher E. Mason, Kasthuri Venkateswaran
    Scientific Reports.2023;[Epub]     CrossRef
  • Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region
    HU PAN, JIE ZHOU, ZHUOMA DAWA, YANNA DAI, YIFAN ZHANG, HUI YANG, CHONG WANG, HUHU LIU, HUI ZHOU, XIANGYANG LU, YUN TIAN
    Polish Journal of Microbiology.2021; 70(1): 87.     CrossRef
  • Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems
    Zobia Khatoon, Suiliang Huang, Mazhar Rafique, Ali Fakhar, Muhammad Aqeel Kamran, Gustavo Santoyo
    Journal of Environmental Management.2020; 273: 111118.     CrossRef
  • Notification of changes in taxonomic opinion previously published outside the IJSEM
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology.2019; 69(1): 13.     CrossRef
Halomonas tibetensis sp. nov., isolated from saline lakes on Tibetan Plateau
Hui-bin Lu , Peng Xing , Lei Zhai , Dorji Phurbu , Qian Tang , Qing-long Wu
J. Microbiol. 2018;56(7):493-499.   Published online June 14, 2018
DOI: https://doi.org/10.1007/s12275-018-8076-5
  • 312 View
  • 0 Download
  • 6 Crossref
AbstractAbstract PDF
Strains pyc13T and ZGT13 were isolated from Lake Pengyan and Lake Zigetang on Tibetan Plateau, respectively. Both strains were Gram-negative, catalase- and oxidase-positive, aerobic, rod-shaped, nonmotile, and nonflagellated bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains pyc13T and ZGT13 belong to the genus Halomonas, with Halomonas alkalicola 56-L4-10aEnT as their closest neighbor, showing 97.4% 16S rRNA gene sequence similarity. The predominant respiratory quinone of both strains was Q-9, with Q-8 as a minor component. The major fatty acids of both strains were C18:1 ω6c/C18:1 ω7c, C16:1 ω6c/C16:1 ω7c, C16:0, and C12:0 3OH. The polar lipids of both strains consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid, phospholipids of unknown structure containing glucosamine, and unidentified phospholipids. The DNA G + C content of pyc13T and ZGT13 were 62.6 and 63.4 mol%, respectively. The DNA-DNA hybridization values of strain pyc13T were 34, 41, 61, 35, and 35% with the reference strains H. alkalicola 56-L4-10aEnT, H. sediminicola CPS11T, H. mongoliensis Z-7009T, H. ventosae Al12T, and H. fontilapidosi 5CRT, respectively. Phenotypic, biochemical, genotypic, and DNA-DNA hybridization data showed that strains pyc13T and ZGT13 represent a new species within the genus Halomonas, for which the name H. tibetensis sp. nov. is proposed. The type strain is pyc13T (= CGMCC 1.15949T = KCTC 52660T).

Citations

Citations to this article as recorded by  
  • The Bacterial Microbiota of Artisanal Cheeses from the Northern Caucasus
    Tatiana V. Kochetkova, Ilya P. Grabarnik, Alexandra A. Klyukina, Kseniya S. Zayulina, Liliya A. Gavirova, Polina A. Shcherbakova, Gennady S. Kachmazov, Andrey I. Shestakov, Ilya V. Kublanov, Alexander G. Elcheninov
    Fermentation.2023; 9(8): 719.     CrossRef
  • Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench
    Fan Wang, Jin-Jian Wan, Xi-Ying Zhang, Yu Xin, Mei-Ling Sun, Peng Wang, Wei-Peng Zhang, Ji-Wei Tian, Yu-Zhong Zhang, Chun-Yang Li, Hui-Hui Fu
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Halomonas jincaotanensis sp. nov., isolated from the Pamir Plateau degrading polycyclic aromatic hydrocarbon
    Xuying Bu, Zhanfeng Xia, Zhanwen Liu, Min Ren, Chuanxing Wan, Lili Zhang
    Archives of Microbiology.2022;[Epub]     CrossRef
  • Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau
    Peixin Gao, Huibin Lu, Peng Xing, Qinglong L. Wu
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(10): 5217.     CrossRef
  • Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau
    Huibin Lu, Peng Xing, Lei Zhai, Huabing Li, Qinglong Wu
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(4): 2859.     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.2018; 68(11): 3379.     CrossRef
Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae
Tuan Manh Nguyen , Ngoc Hoang Trinh , Jaisoo Kim
J. Microbiol. 2018;56(7):485-492.   Published online June 14, 2018
DOI: https://doi.org/10.1007/s12275-018-8025-3
  • 325 View
  • 0 Download
  • 9 Crossref
AbstractAbstract PDF
Three novel bacterial strains (UCM-2T, UCM-G28T, and UCM-G35T) were obtained while isolating soil bacteria for the development of antibiotics. Cells of these strains were Gram-negative, non-spore forming, motile by means of a single flagellum, and rod shaped. In all strains, the predominant isoprenoid quinone was ubiquinone-8 (Q-8). Cells contained C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and C17:0 cyclo as the major fatty acids, and C10:0 3-OH as the major hydroxy fatty acid. The polar lipid profiles of the three novel strains were dominated by diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C contents of strains UCM-2T, UCM-G28T, and UCMG35T were 67.5, 65.9, and 66.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA sequences showed that strain UCM-2T was most closely related to Variovorax soli NBRC 106424T, whereas strains UCM-G28T and UCM-G35T were most similar to Variovorax ginsengisoli Gsoil 3165T. Values indicating DNA-DNA hybridization between the novel isolates and closely related species in the genus Variovorax were lower than the 70% cut-off point. These phenotypic, chemotaxonomic, and phylogenetic data indicate that the three isolates should be classified as new members of the genus Variovorax, for which the names Variovorax ureilyticus sp. nov., Variovorax rhizosphaerae sp. nov., and Variovorax robiniae sp. nov. are proposed. The type strains are UCM-2T (= KACC 18899T = NBRC 112306T), UCMG28T (= KACC 18900T = NBRC 112307T), and UCM-G35T (= KACC 18901T = NBRC 112308T), respectively.

Citations

Citations to this article as recorded by  
  • Encephalartos natalensis association with non-cyanobacterial species increased reliance on atmospheric nitrogen in acidic and nutrient-deficient savanna woodland ecosystem soils
    Siphelele Ndlovu, Nqobile Motsomane, Terence Suinyuy, Anathi Magadlela
    Transactions of the Royal Society of South Africa.2024; 79(3): 203.     CrossRef
  • The first reported case of human infection with Variovorax durovernensis; a novel Variovorax sp. Isolated from the prosthetic aortic graft of a shepherd
    Lara Payne, Adela Alcolea-Medina, Luke B Snell, Christopher Alder, Themoula Charalampous, Jake D Turnbull, Jonathan D Edgeworth, Rahul Batra, John L Klein, Anna L Goodman
    Clinical Infection in Practice.2024; 21: 100332.     CrossRef
  • Encephalartos natalensis, Their Nutrient-Cycling Microbes and Enzymes: A Story of Successful Trade-Offs
    Siphelele Ndlovu, Terence N. Suinyuy, María A. Pérez-Fernández, Anathi Magadlela
    Plants.2023; 12(5): 1034.     CrossRef
  • Variovorax durovernensis sp. nov., a novel species isolated from an infected prosthetic aortic graft in a human
    Adela Alcolea-Medina, Luke B. Snell, Lara Payne, Christopher J. Alder, Jake D. Turnbull, Themoula Charalampous, Lisa Bryan, John L. Klein, Jonathan D. Edgeworth, Rahul Batra, Anna L. Goodman
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity
    Chae Yung Woo, Jaisoo Kim
    Journal of Microbiology and Biotechnology.2022; 32(7): 855.     CrossRef
  • Full Issue PDF

    Phytobiomes Journal.2021; 5(1): 1.     CrossRef
  • Nitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass Roots
    Rahul A. Bahulikar, Srinivasa R. Chaluvadi, Ivone Torres-Jerez, Jagadish Mosali, Jeffrey L. Bennetzen, Michael Udvardi
    Phytobiomes Journal.2021; 5(1): 80.     CrossRef
  • Variovorax beijingensis sp. nov., a novel plant-associated bacterial species with plant growth-promoting potential isolated from different geographic regions of Beijing, China
    Jun-lian Gao, Yu-chen Sun, Jing Xue, Pengbo Sun, Hui Yan, Mohammad Sayyar Khan, Li-wei Wang, Xiuhai Zhang, Jian-guang Sun
    Systematic and Applied Microbiology.2020; 43(6): 126135.     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.2018; 68(11): 3379.     CrossRef
Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka
Pratiksha Behera , Madhusmita Mahapatra , Arman Seuylemezian , Parag Vaishampayan , V. Venkata Ramana , Neetha Joseph , Amaraja Joshi , Yogesh Shouche , Mrutyunjay Suar , Ajit K. Pattnaik , Gurdeep Rastogi
J. Microbiol. 2018;56(7):458-466.   Published online June 14, 2018
DOI: https://doi.org/10.1007/s12275-018-7549-x
  • 344 View
  • 0 Download
  • 7 Crossref
AbstractAbstract PDF
The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11T , isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045T (99.29%), Pseudomonas toyotomiensis JCM 15604T (99.15%), Pseudomonas chengduensis DSM 26382T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016T (99.08%), and Pseudomonas alcaliphila JCM 10630T (99.01%). Experimental DNA-DNA relatedness between strain PI11T and P. indoloxydans JCM 14246T was 49.4%. The draft genome of strain PI11T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C18:1 ω6c/ω7c, C16:1 ω6c/ω7c, and C16:0. The DNA G + C content of strain PI11T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11T was delineated from other closely related type strains. It is proposed that strain PI11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11T (= KCTC 42576T = DSMZ 100245T).

Citations

Citations to this article as recorded by  
  • Removal of Nitrogen and Phosphorus by a Novel Salt-Tolerant Strain Pseudomonas sediminis D4
    Yuting Liu, Peng Yin, Jiayi Zhou, Yonghao Ma, Xunheng Lai, Junduo Lin, Huilin Peng, Hu Shu, Wen Huang
    Water.2025; 17(4): 502.     CrossRef
  • Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera
    Bashudev Rudra, Radhey S. Gupta
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Plant growth-promoting characteristics of halotolerant endophytic bacteria isolated from Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. of Ethiopian rift valley lakes
    Solomon Enquahone, Guido van Marle, Addis Simachew
    Archives of Microbiology.2022;[Epub]     CrossRef
  • Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment
    Eui-Sang Cho, In-Tae Cha, Seong Woon Roh, Myung-Ji Seo
    Antonie van Leeuwenhoek.2021; 114(12): 2065.     CrossRef
  • Pseudomonas carbonaria sp. nov., isolated from charcoal
    Peter Kämpfer, S. P. Glaeser, John A. McInroy, Dominique Clermont, Alexis Criscuolo, Hans-Jürgen Busse
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar salt
    Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Se Hee Lee, Na-Ri Shin, Jin-Woo Bae, Jinjong Myoung, Ki-Eun Lee, In-Tae Cha, Jin-Kyu Rhee, Seong Woon Roh
    Systematic and Applied Microbiology.2020; 43(3): 126085.     CrossRef
  • Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
    Young Joon Oh, Joon Yong Kim, Hyo Kyeong Park, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2019; 57(11): 997.     CrossRef
Bacillus ferrooxidans sp. nov., an iron(II)-oxidizing bacterium isolated from paddy soil
Guo-Wei Zhou , Xiao-Ru Yang , Jian-Qiang Su , Bang-Xiao Zheng , Yong-Guan Zhu
J. Microbiol. 2018;56(7):472-477.   Published online June 14, 2018
DOI: https://doi.org/10.1007/s12275-018-7543-3
  • 316 View
  • 0 Download
  • 5 Crossref
AbstractAbstract PDF
An endospore-forming bacterium, designated YT-3T, was isolated from a paddy soil in Yingtan, Jiangxi, China. Cells of strain YT-3T were Gram-positive, rod-shaped, facultative anaerobic, catalase, and oxidase positive. The optimum growth temperature and pH were 30°C (ranged from 15 to 50°C) and 6.5–7.0 (ranged from 3 to 11), respectively. Analysis of the 16S rRNA gene sequence showed that strain YT-3T was affiliated to the genus Bacillus and displayed the highest similarity to that of Bacillus drentensis JCM 21707T (98.3%), followed by B. ginsengisoli JCM 17335T (97.8%) and B. fumarioli JCM 21708T (97.0%). The similarity of rpoB gene sequence between strain YT-3T and B. drentensis JCM 21707T, B. ginsengisoli JCM 17335T and B. fumarioli JCM 21708T was 80.4%, 81.5%, and 82.1%, respectively. The genomic DNA G + C content was 44.9 mol%. The predominant respiratory quinone was Menaquinone-7, and meso-diaminopimelic acid was present in the peptidoglycan layer of cell wall. The major fatty acids were C15:0 anteiso (36.2%), C14:0 iso (19.6%), C15:0 iso (17.4%), and C16:0 iso (9.8%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and ammoniac phospholipids. The DNA-DNA hybridization values between isolate YT-3T and B. drentensis (JCM 21707T), B. ginsengisoli (JCM 17335T), and B. fumarioli (JCM 21708T) were 36.3%, 30.3%, and 25.3%, respectively. On the basis of physiological, genetic and biochemical data, strain YT-3T represented a novel species of the genus Bacillus, for which the name Bacillus ferrooxidans sp. nov was proposed. The type strain is YT-3T (= KCTC 33875T = CCTCC AB 2017049T).

Citations

Citations to this article as recorded by  
  • Nitrate addition in different anoxic stages of acid paddy soil and the impacts on cadmium immobilization
    Hanbing Meng, Shan Wang, Yang Yang, Zebin Hong, Shiwen Hu, Guojun Chen, Kuan Cheng, Tongxu Liu
    Chemical Geology.2025; 690: 122867.     CrossRef
  • Discarded masks as hotspots of antibiotic resistance genes during COVID-19 pandemic
    Shu-Yi-Dan Zhou, Chenshuo Lin, Kai Yang, Le-Yang Yang, Xiao-Ru Yang, Fu-Yi Huang, Roy Neilson, Jian-Qiang Su, Yong-Guan Zhu
    Journal of Hazardous Materials.2022; 425: 127774.     CrossRef
  • Underestimation about the Contribution of Nitrate Reducers to Iron Cycling Indicated by Enterobacter Strain
    Ming-Jun Li, Meng-Yun Wei, Xiao-Ting Fan, Guo-Wei Zhou
    Molecules.2022; 27(17): 5581.     CrossRef
  • Fe toxicity in plants: Impacts and remediation
    Noreen Zahra, Muhammad Bilal Hafeez, Kanval Shaukat, Abdul Wahid, Mirza Hasanuzzaman
    Physiologia Plantarum.2021;[Epub]     CrossRef
  • Metabolic Inactivity and Re-awakening of a Nitrate Reduction Dependent Iron(II)-Oxidizing Bacterium Bacillus ferrooxidans
    Guo-Wei Zhou, Xiao-Ru Yang, Regin Rønn, Jian-Qiang Su, Li Cui, Bang-Xiao Zheng, Yong-Guan Zhu
    Frontiers in Microbiology.2019;[Epub]     CrossRef
Journal of Microbiology : Journal of Microbiology
© The Microbiological Society of Korea.
TOP