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Characterization of novel bacteriophages for effective phage therapy against Vibrio infections in aquaculture
Kira Moon, Sangdon Ryu, Seung Hui Song, Se Won Chun, Nakyeong Lee, Aslan Hwanhwi Lee
J. Microbiol. 2025;63(5):e2502009.   Published online May 27, 2025
DOI: https://doi.org/10.71150/jm.2502009
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AbstractAbstract PDFSupplementary Material

The widespread use of antibiotics in aquaculture has led to the emergence of multidrug-resistant pathogens and environmental concerns, highlighting the need for sustainable, eco-friendly alternatives. In this study, we isolated and characterized three novel bacteriophages from aquaculture effluents in Korean shrimp farms that target the key Vibrio pathogens, Vibrio harveyi, and Vibrio parahaemolyticus. Bacteriophages were isolated through environmental enrichment and serial purification using double-layer agar assays. Transmission electron microscopy revealed that the phages infecting V. harveyi, designated as vB_VhaS-MS01 and vB_VhaS-MS03, exhibited typical Siphoviridae morphology with long contractile tails and icosahedral heads, whereas the phage isolated from V. parahaemolyticus (vB_VpaP-MS02) displayed Podoviridae characteristics with an icosahedral head and short tail.

Whole-genome sequencing produced complete, circularized genomes of 81,710 bp for vB_VhaS-MS01, 81,874 bp for vB_VhaS-MS03, and 76,865 bp for vB_VpaP-MS02, each showing a modular genome organization typical of Caudoviricetes. Genomic and phylogenetic analyses based on the terminase large subunit gene revealed that although vB_VhaS-MS01 and vB_VhaS-MS03 were closely related, vB_VpaP-MS02 exhibited a distinct genomic architecture that reflects its unique morphology and host specificity. Collectively, these comparative analyses demonstrated that all three phages possess genetic sequences markedly different from those of previously reported bacteriophages, thereby establishing their novelty. One-step growth and multiplicity of infection (MOI) experiments demonstrated significant differences in replication kinetics, such as burst size and lytic efficiency, among the phages, with vB_VhaS-MS03 maintaining the most effective bacterial control, even at an MOI of 0.01. Additionally, host range assays showed that vB_VhaS-MS03 possessed a broader spectrum of activity, supporting its potential use as a stand-alone agent or key component of phage cocktails. These findings highlight the potential of region-specific phage therapy as a targeted and sustainable alternative to antibiotics for controlling Vibrio infections in aquaculture.

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  • Feed Additives in Aquaculture: Benefits, Risks, and the Need for Robust Regulatory Frameworks
    Ekemini Okon, Matthew Iyobhebhe, Paul Olatunji, Mary Adeleke, Nelson Matekwe, Reuben Okocha
    Fishes.2025; 10(9): 471.     CrossRef
Journal Article
Comparative Secretory Efficiency of Two Chitosanase Signal Peptides from Bacillus subtilis in Escherichia coli
Tae-Yang Eom, Yehui Gang, Youngdeuk Lee, Yoon-Hyeok Kang, Eunyoung Jo, Svini Dileepa Marasinghe, Heung Sik Park, Gun-Hoo Park, Chulhong Oh
J. Microbiol. 2024;62(12):1155-1164.   Published online November 25, 2024
DOI: https://doi.org/10.1007/s12275-024-00186-1
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AbstractAbstract PDF
The production of recombinant proteins in Escherichia coli is often challenged by cytoplasmic expression due to proteolytic degradation and inclusion body formation. Extracellular expression can overcome these problems by simplifying downstream processing and improving protein yields. This study aims to compare the efficiency of two Bacillus subtilis chitosanase signal peptides in mediating extracellular secretion in E. coli. We identified a naturally occurring mutant signal peptide (mCsn2-SP) from B. subtilis CH2 chitosanase (CH2CSN), which is characterized by a deletion of six amino acids in the N-region relative to the signal peptide (Csn1-SP) from B. subtilis CH1 chitosanase (CH1CSN). The CH1CSN and CH2CSN genes were cloned into the pET-11a vector and protein secretion was evaluated in E. coli BL21(DE3) host cells. Expression was induced with 0.1 mM and 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) at 30 °C for one and three days. CH2CSN showed higher secretion levels compared to CH1CSN under all experimental conditions, especially with 0.1 mM IPTG induction for 3 days, which resulted in a 2.37-fold increase in secretion. Furthermore, it was demonstrated that mCsn2-SP is capable of secreting human Cu,Zn-superoxide dismutase (hSOD) in E. coli BL21(DE3) and successfully translocating it to the periplasmic region. This study represents the inaugural investigation into the utilisation of a naturally modified signal peptide, thereby corroborating the assertion that signal peptide deletion variants can influence protein secretion efficiency. Furthermore, the findings substantiate the proposition that such variants can serve as a viable alternative for the secretion of heterologous proteins in E. coli.

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  • Signal Peptides: From Molecular Mechanisms to Applications in Protein and Vaccine Engineering
    Shuai Zhang, Zhihui He, Hui Wang, Jingbo Zhai
    Biomolecules.2025; 15(6): 897.     CrossRef
Review
Fecal Microbiota Transplantation: Indications, Methods, and Challenges.
Jee Young Lee, Yehwon Kim, Jiyoun Kim, Jiyeun Kate Kim
J. Microbiol. 2024;62(12):1057-1074.   Published online November 18, 2024
DOI: https://doi.org/10.1007/s12275-024-00184-3
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AbstractAbstract PDF
Over the past two decades, as the importance of gut microbiota to human health has become widely known, attempts have been made to treat diseases by correcting dysbiosis of gut microbiota through fecal microbiota transplantation (FMT). Apart from current knowledge of gut microbiota, FMT to treat disease has a long history, from the treatment of food poisoning in the fourth century to the treatment of Clostridioides difficile infections in the twentieth century. In 2013, FMT was recognized as a standard treatment for recurrent C. difficile because it consistently showed high efficacy. Though recurrent C. difficile is the only disease internationally recognized for FMT efficacy, FMT has been tested for other diseases and shown some promising preliminary results. Different FMT methods have been developed using various formulations and administration routes. Despite advances in FMT, some issues remain to be resolved, such as donor screening, manufacturing protocols, and unknown components in the fecal microbiota. In this review, we discuss the mechanisms, clinical indications, methods, and challenges of current FMT. We also discuss the development of alternative therapies to overcome the challenges of FMT.

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Citations to this article as recorded by  
  • Transplantation of Fecal Flora from Patients with Atherosclerosis to Mice Can Increase Serum Low-Density Lipoprotein Cholesterol and Affect Intestinal Flora and Its Metabolites
    Liang Feng, Jianting Feng, Li He, Fu Chen, Xin Feng, Suwen Wang
    Applied Microbiology.2025; 5(1): 29.     CrossRef
  • Management of refractory checkpoint inhibitor-induced colitis
    Anas Zaher, Maria Julia Moura Nascimento Santos, Hassan Elsaygh, Stephen J. Peterson, Carolina Colli Cruz, Anusha Shirwaikar Thomas, Yinghong Wang
    Expert Opinion on Drug Safety.2025; : 1.     CrossRef
  • Fecal Microbiota Transplantation (FMT) in Clostridium difficile Infection: A Paradigm Shift in Gastrointestinal Microbiome Modulation
    Muhammad Hamza Saeed, Sundas Qamar, Ayesha Ishtiaq, Qudsia Umaira khan, Asma Atta, Maryam Atta, Hifza Ishtiaq, Marriam Khan, Muhammad Rawal Saeed, Ayesha Iqbal
    Cureus.2025;[Epub]     CrossRef
  • Exploring the gut microbiome’s influence on cancer-associated anemia: Mechanisms, clinical challenges, and innovative therapies
    Ayrton Bangolo, Behzad Amoozgar, Maryam Habibi, Elizabeth Simms, Vignesh K Nagesh, Shruti Wadhwani, Nikita Wadhwani, Auda Auda, Daniel Elias, Charlene Mansour, Robert Abbott, Nisrene Jebara, Lili Zhang, Sarvarinder Gill, Kareem Ahmed, Andrew Ip, Andre Goy
    World Journal of Gastrointestinal Pharmacology and Therapeutics.2025;[Epub]     CrossRef
  • Microbiome Therapeutics for Clostridioides difficile Infection
    Christine W. Lucky, Rachel L. Medernach, Brendan J. Kelly, Jennie H. Kwon, Michael H. Woodworth
    Infectious Disease Clinics of North America.2025; 39(4): 663.     CrossRef
  • Laboratory preparation methods for human-derived fecal microbial suspensions for fecal microbiota transplantation: a review and standardization perspectives
    Jinhua Gong, Yuchi Liu, Liuye Huang
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention
    Furong Ba, Wei Wang, Yilun Huang, Shuobo Zhang, Bo Qiu, Siyuan Xie, Lvwan Xu, Wang Gao, Xiaoqin Zhang, Zhenyu Wen, Qifan Wang, Hainv Gao, Guoping Sheng, Björn Berglund, Ping Li, Lanjuan Li, Mingfei Yao
    Microbiome.2025;[Epub]     CrossRef
  • Fecal microbiota transplantation as salvage therapy for disseminated strongyloidiasis in an immunosuppressed patient: a case report
    Wei Fu, Na Peng, Yan Geng
    Frontiers in Immunology.2025;[Epub]     CrossRef
Journal Articles
Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa
Koketso Desiree Mazwi, Kgaugelo Edward Lekota, Barbara Akofo Glover, Francis Babaman Kolo, Ayesha Hassim, Jenny Rossouw, Annelize Jonker, Justnya Maria Wojno, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio, Katiuscia Zilli, Anna Janowicz, Francesca Marotta, Giuliano Garofolo, Henriette van Heerden
J. Microbiol. 2024;62(9):759-773.   Published online July 22, 2024
DOI: https://doi.org/10.1007/s12275-024-00155-8
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AbstractAbstract PDF
Brucellosis is an economically important zoonotic disease affecting humans, livestock, and wildlife health globally and especially in Africa. Brucella abortus and B. melitensis have been isolated from human, livestock (cattle and goat), and wildlife (sable) in South Africa (SA) but with little knowledge of the population genomic structure of this pathogen in SA. As whole genome sequencing can assist to differentiate and trace the origin of outbreaks of Brucella spp. strains, the whole genomes of retrospective isolates (n = 19) from previous studies were sequenced. Sequences were analysed using average nucleotide identity (ANI), pangenomics, and whole genome single nucleotide polymorphism (wgSNP) to trace the geographical origin of cases of brucellosis circulating in human, cattle, goats, and sable from different provinces in SA. Pangenomics analysis of B. melitensis (n = 69) and B. abortus (n = 56) was conducted with 19 strains that included B. abortus from cattle (n = 3) and B. melitensis from a human (n = 1), cattle (n = 1), goat (n = 1), Rev1 vaccine strain (n = 1), and sable (n = 12). Pangenomics analysis of B. melitensis genomes, highlighted shared genes, that include 10 hypothetical proteins and genes that encodes for acetyl-coenzyme A synthetase (acs), and acylamidase (aam) amongst the sable genomes. The wgSNP analysis confirmed the B. melitensis isolated from human was more closely related to the goat from the Western Cape Province from the same outbreak than the B. melitensis cattle sample from different cases in the Gauteng Province. The B. melitensis sable strains could be distinguished from the African lineage, constituting their own African sub-clade. The sequenced B. abortus strains clustered in the C2 lineage that is closely related to the isolates from Mozambique and Zimbabwe. This study identified genetically diverse Brucella spp. among various hosts in SA. This study expands the limited known knowledge regarding the presence of B. melitensis in livestock and humans in SA, further building a foundation for future research on the distribution of the Brucella spp. worldwide and its evolutionary background.

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  • Tracing the invisible: Spatial patterns of swine brucellosis in wildlife and domestic pigs of northeast Portugal
    Zita Martins Ruano, Teresa Letra Mateus, José Aranha, Eirini Fragkiadaki, Georgia Tzouganatou, Emmanouil Angelakis, Luís Félix, Jorge Pereira, Ana Chorense, Claudia Rocha, Dulce Loureiro, Ricardo Marcos, Madalena Vieira-Pinto
    The Veterinary Journal.2025; 314: 106464.     CrossRef
  • Limited genomic diversity and convergent adaptation of Brucella melitensis isolated from human in East China, from 2011 to 2024
    Lan Huang, Lu Zhou, Nan Zhang, Weizhong Zhou, Buyun Xu, Jie Hong, Wei Zhang, Ying Zhang, Ke Xu, Changjun Bao, Hai Jiang, Zhongming Tan, Jingxin Li
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • Whole-Genome Sequencing of Brucella melitensis Isolates from Kuwait for the Identification of Biovars, Variants, and Relationship within a Biovar
    Abu Salim Mustafa, Mohd Wasif Khan, Nazima Habibi, Wadha Alfouzan
    Medical Principles and Practice.2024; 34(2): 152.     CrossRef
Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment
Sidra Erum Ishaq, Tariq Ahmad, Lewen Liang, Ruize Xie, Tiantian Yu, Yinzhao Wang, Fengping Wang
J. Microbiol. 2024;62(8):611-625.   Published online July 10, 2024
DOI: https://doi.org/10.1007/s12275-024-00145-w
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AbstractAbstract PDF
Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

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  • Engineering the phycosphere: fundamental concepts and tools for the bottom-up design of microalgal-bacterial consortia
    Austin Semple, Jagroop Pandhal
    Applied Phycology.2025; 6(1): 21.     CrossRef
  • Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea
    Abhay B. Fulke, Nilkanth Sharma, Jayshree Nadekar
    Microbial Ecology.2025;[Epub]     CrossRef
  • The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential
    Inmaculada Tocino-Márquez, Martin Zehl, Joana Séneca, Petra Pjevac, Manuel Felkl, Christian F. W. Becker, Alexander Loy, Thomas Rattei, Andrew N. Ostrovsky, Sergey B. Zotchev
    Scientific Reports.2025;[Epub]     CrossRef
  • Uncertainty Analysis of Biogas Generation and Gas Hydrate Accumulations in the Baiyun Sag, South China Sea
    Pibo Su, Jinqiang Liang, Huai Cheng, Yaoyao Lv, Wei Zhang, Zuofei Zhu
    Microorganisms.2024; 13(1): 5.     CrossRef
Pannonibacter tanglangensis sp. nov., a New Species Isolated from Pond Sediment
Lei Wang, Yanpeng Cheng, Panpan Yang, Jinjin Zhang, Gui Zhang, Sihui Zhang, Jing Yang, Zhen Zhang, Lulu Hu, Ji Pu, Yanying Yang, Xin-He Lai, Jianguo Xu, Yinghui Li, Qinghua Hu
J. Microbiol. 2024;62(9):727-737.   Published online July 5, 2024
DOI: https://doi.org/10.1007/s12275-024-00151-y
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AbstractAbstract PDF
Two bacterial strains (XCT-34T and XCT-53) isolated from sediment samples of an artificial freshwater reservoir were analyzed using a polyphasic approach. The two isolates are aerobic, Gram-stain-negative, oxidase-negative, catalase-positive, motile with polar flagella, rod-shaped, and approximately 1.4-3.4 × 0.4-0.9 μm in size. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences showed that the two strains formed a distinct branch within the evolutionary radiation of the genus Pannonibacter, closest to Pannonibacter carbonis Q4.6T (KCTC 52466). Furthermore, lower than threshold average nucleotide identity values (ANI, 85.7-86.4%) and digital DNA-DNA hybridization values (dDDH, 22.3-30.5%) of the two strains compared to the nearest type strains also confirmed that they represented a novel species. Genomic analyses, including annotation of the KEGG pathways, prediction of the secondary metabolism biosynthetic gene clusters and PHI phenotypes, supported functional inference and differentiation of the strains from the closely related taxa. Results of chemotaxonomic and physiological studies revealed that their distinct phenotypic characteristics distinguished them from existing Pannonibacter species. Thus, the two strains are considered to represent a novel species of Pannonibacter, for which the name of Pannonibacter tanglangensis sp. nov. is proposed, with XCT-34T (= KCTC 82332T = GDMCC 1.1947T) as the respective type strain.

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  • 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
Review
The Role of Extracellular Vesicles in Pandemic Viral Infections
Woosung Shim, Anjae Lee, Jung-Hyun Lee
J. Microbiol. 2024;62(6):419-427.   Published online June 25, 2024
DOI: https://doi.org/10.1007/s12275-024-00144-x
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AbstractAbstract PDF
Extracellular vesicles (EVs), of diverse origin and content, are membranous structures secreted by a broad range of cell types. Recent advances in molecular biology have highlighted the pivotal role of EVs in mediating intercellular communication, facilitated by their ability to transport a diverse range of biomolecules, including proteins, lipids, DNA, RNA and metabolites. A striking feature of EVs is their ability to exert dual effects during viral infections, involving both proviral and antiviral effects. This review explores the dual roles of EVs, particularly in the context of pandemic viruses such as HIV-1 and SARS-CoV-2. On the one hand, EVs can enhance viral replication and exacerbate pathogenesis by transferring viral components to susceptible cells. On the other hand, they have intrinsic antiviral properties, including activation of immune responses and direct inhibition of viral infection. By exploring these contrasting functions, our review emphasizes the complexity of EV-mediated interactions in viral pathogenesis and highlights their potential as targets for therapeutic intervention. The insights obtained from investigating EVs in the context of HIV-1 and SARS-CoV-2 provide a deeper understanding of viral mechanisms and pathologies, and offer a new perspective on managing and mitigating the impact of these global health challenges.

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  • Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants
    Tae-Hun Kim, Sojung Bae, Jinjong Myoung
    Journal of Microbiology and Biotechnology.2024; 34(12): 2506.     CrossRef
Journal Article
Genetically Engineered CLDN18.2 CAR-T Cells Expressing Synthetic PD1/CD28 Fusion Receptors Produced Using a Lentiviral Vector
Heon Ju Lee, Seo Jin Hwang, Eun Hee Jeong, Mi Hee Chang
J. Microbiol. 2024;62(7):555-568.   Published online May 3, 2024
DOI: https://doi.org/10.1007/s12275-024-00133-0
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AbstractAbstract PDF
This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1. CLDN18.2, a gastric-specific membrane protein, is considered a potential therapeutic target for gastric and other cancers. In our study, CLDN18.2 CAR was a second-generation CAR with inducible T-cell costimulatory (CD278), and CLDN18.2-PD1/CD28 CAR was a third-generation CAR, wherein the synthetic PD1/CD28 chimeric-switch receptor (CSR) was added to the second-generation CAR. In vitro, we detected the secretion levels of different cytokines and the killing ability of CAR-T cells. We found that the secretion of cytokines such as interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) secreted by three types of CAR-T cells was increased, and the killing ability against CLDN18.2-positive GC cells was enhanced. In vivo, we established a xenograft GC model and observed the antitumor effects and off-target toxicity of CAR-T cells. These results support that synthetic anti-CLDN18.2 CAR-T cells have antitumor effect and anti-CLDN18.2-PD1/CD28 CAR could provide a promising design strategy to improve the efficacy of CAR-T cells in advanced gastric cancer.

Citations

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  • Enhancing the antitumor activity of CD19/BCMA CAR-T cells in vitro with a PD1IL7R chimeric switch receptor
    Kai Yan, Zhongdang Xiao
    Cellular Immunology.2025; 415-416: 105001.     CrossRef
  • Research progress on mechanisms of tumor immune microenvironment and gastrointestinal resistance to immunotherapy: mini review
    Zheng Zhang, Yangping Wu
    Frontiers in Immunology.2025;[Epub]     CrossRef
  • On-target off-tumor toxicity of claudin18.2-directed CAR-T cells in preclinical models
    Filippo Birocchi, Antonio J. Almazan, Aiyana Parker, Amanda A. Bouffard, Sadie Goncalves, Christopher Kelly, Jessica Frank, Mark B. Leick, Nicholas J. Haradhvala, Shaw Kagawa, Gad Getz, Giulia Escobar, Diego Salas-Benito, Adele Mucci, Trisha R. Berger, Ma
    Nature Communications.2025;[Epub]     CrossRef
Review
Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater—A Review
Sua Lee , Min Cho , Michael J. Sadowsky , Jeonghwan Jang
J. Microbiol. 2023;61(9):791-805.   Published online August 18, 2023
DOI: https://doi.org/10.1007/s12275-023-00067-z
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AbstractAbstract PDF
Nitrate ( NO3 −) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3 − have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas ( N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3 −-removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3 − in several field studies. NO3 − removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3 − to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3 − pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3 − from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3 − in WBR, and perspectives to enhance WBR performance in the future.

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  • Complete genome sequence of Neobacillus sp. strain OS1-2, a denitrifying bacterium isolated from apple orchard soil
    Jinwoo Ahn, Jeonghwan Jang, Elinne Becket
    Microbiology Resource Announcements.2025;[Epub]     CrossRef
  • Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition
    Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang
    Journal of Microbiology.2025; 63(2): e2411019.     CrossRef
  • Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater
    Xinyue Gong, Qin Peng, Ruixin Jiang, Na Yang, Cijun Xing, Rui Wang
    Journal of Hazardous Materials.2025; 488: 137383.     CrossRef
  • Impact of projective soil cover with post-harvest residues on soil microbiological indicators in the conditions of the Left-Bank Forest-Steppe of Ukraine
    Z. O. Dehtiarova, A. A. Dyomkin
    Man and Environment. Issues of Neoecology.2025; (43): 147.     CrossRef
Journal Articles
UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction
Seong-In Na , Michael James Bailey , Mauricio Chalita , Jae Hyoung Cho , Jongsik Chun
J. Microbiol. 2023;61(7):683-692.   Published online August 11, 2023
DOI: https://doi.org/10.1007/s12275-023-00064-2
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AbstractAbstract PDF
In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard
method
. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https:// www. ezbio cloud. net/ tools/ uacg.

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  • Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
    Raúl Riesco, Martha E. Trujillo
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
Relationship Between Mycotoxin Production and Gene Expression in Fusarium graminearum Species Complex Strains Under Various Environmental Conditions
Wenwen Huang , Ping Zhou , Guanghui Shen , Tao Gao , Xin Liu , Jianrong Shi , Jianhong Xu , Jianbo Qiu
J. Microbiol. 2023;61(5):525-542.   Published online May 2, 2023
DOI: https://doi.org/10.1007/s12275-023-00046-4
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AbstractAbstract PDF
The Fusarium graminearum species complex (FGSC) can produce various mycotoxins and is a major concern for food quantity and quality worldwide. In this study, we determined the effects of water activity ( aw), temperature, incubation time and their interactions on mycotoxin accumulation and the expression levels of biosynthetic genes in FGSC strains from maize samples in China. The highest deoxynivalenol (DON), 3-acetyldeoxynivalenol(3ADON) and 15-acetyldeoxynivalenol (15ADON) levels of the F. boothii and F. graminearum strains were observed at 0.98 aw/ 30 °C or 0.99 aw/ 25 °C. F. asiaticum and F. meridionale reached maximum nivalenol (NIV) and 4-acetylnivalenol (4ANIV) contents at 0.99 aw and 30 °C. With the extension of the incubation time, the concentrations of DON and NIV gradually increased, while those of their derivatives decreased. F. boothii, F. meridionale and one F. asiaticum strain had the highest zearalenone (ZEN) values at 0.95 aw and 25 °C, while the optimum conditions for the other F. asiaticum strain and F. graminearum were 0.99 aw and 30 °C. Four genes associated with trichothecene and zearalenone synthesis were significantly induced under higher water stress in the early stage of production. The results indicated independence of mycotoxin production and gene expression, as maximum amounts of these toxic metabolites were observed at higher aw in most cases. This study provides useful information for the monitoring and prevention of such toxins entering the maize production chain.

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  • Geographic variations in the Fusarium species and toxins associated with maize ear rot in China
    Jianbo Qiu, Can Jiang, Shufang Wang, Can He, Daoming Chen, Jing Lan, Jianhong Xu, Yin-Won Lee, Jianrong Shi
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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
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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.

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  • 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
Vaginal Microbiome Dysbiosis is Associated with the Different Cervical Disease Status
Yingying Ma , Yanpeng Li , Yanmei Liu , Le Cao , Xiao Han , Shujun Gao , Chiyu Zhang
J. Microbiol. 2023;61(4):423-432.   Published online April 3, 2023
DOI: https://doi.org/10.1007/s12275-023-00039-3
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AbstractAbstract PDF
Vaginal microbiome composition was demonstrated to be associated with cervical disease. The colonization characteristics of vaginal microbes and their association with the different cervical disease status, especially cervical cancer (CC), are rarely investigated. In this cross-sectional study, we characterized the vaginal microbiome of women with different status of cervical diseases, including 22 NV + (normal tissue with HPV infection), low-grade squamous intraepithelial lesion (LSIL, n = 45), high-grade squamous intraepithelial lesion (HSIL, n = 36) and CC (n = 27) using bacterial 16S DNA sequencing. Thirty HPV-negative women with normal tissue were used as the control group. We found that higher diversity of microbiome with gradual depletion of Lactobacillus, especially L. crispatus, was associated with the severity of cervical disease. High-risk HPV16 infection was associated with higher microbiome diversity and depletion of Lactobacillus in high-grade cervical diseases (i.e. HSIL and CC). The CC group was characterized by higher levels of Fannyhessea vaginae, Prevotella, Bacteroides, Finegoldia, Vibrio, Veillonella, Peptostreptococcus, and Dialister. Co-occurrence network analyses showed that negative correlations were exclusively observed between Lactobacillus and other bacteria, and almost all non-Lactobacillus bacteria were positively correlated with each other. In particular, the most diverse and complex co-occurrence network of vaginal bacteria, as well as a complete loss of L. crispatus, was observed in women with CC. Logistic regression model identified HPV16 and Lactobacillus as significant risk and protective factors for CC, respectively. These results suggest that specific Lactobacillus species (e.g. L. crispatus and L. iners) can be used as important markers to target prevention measures prioritizing HPV16-infected women and other hrHPV-infected women for test, vaccination and treat initiatives.

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  • Vaginal Microbiota and Local Immunity in HPV-Induced High-Grade Cervical Dysplasia: A Narrative Review
    Helena C. J. Schellekens, Lotte M. S. Schmidt, Servaas A. Morré, Edith M. G. van Esch, Peggy J. de Vos van Steenwijk
    International Journal of Molecular Sciences.2025; 26(9): 3954.     CrossRef
  • The Vaginal Microbiota, Human Papillomavirus, and Cervical Dysplasia—A Review
    Justė Kazlauskaitė, Guoda Žukienė, Vilius Rudaitis, Daiva Bartkevičienė
    Medicina.2025; 61(5): 847.     CrossRef
  • Nanoparticles and the Vaginal Microbiota: Diagnostic and Therapeutic Innovations in Human Papilloma Virus-associated Cervical Cancer – A Systematic Review
    Saranya Velmurugan, Karthikeyan Ganesan, Archana Rajasundaram, C. Thangam, Rozario Cyril, Gowtham Kumar Subbaraj
    Nigerian Postgraduate Medical Journal.2025; 32(1): 1.     CrossRef
  • Exploring the Interplay Between Cervicovaginal Microbiome, HPV Infection, and Cervical Intraepithelial Neoplasia in Taiwanese Women
    Chung‐Yao Yang, Ting‐Chang Chang, Yi‐Tzu Lee, Ting‐Ying Shih, Chang‐Wei Li, Chao‐Min Cheng
    Journal of Medical Virology.2025;[Epub]     CrossRef
  • A nomogram prediction model for embryo implantation outcomes based on the cervical microbiota of the infertile patients during IVF-FET
    Yanan Wu, Lingyun Shi, Zili Jin, Wenjun Chen, Fuxin Wang, Huihua Wu, Hong Li, Ce Zhang, Rui Zhu, Simone Filardo
    Microbiology Spectrum.2025;[Epub]     CrossRef
  • The Interplay Between Cervicovaginal Microbiota Diversity, Lactobacillus Profiles and Human Papillomavirus in Cervical Cancer: A Systematic Review
    Giosuè Giordano Incognito, Carlo Ronsini, Vittorio Palmara, Paola Romeo, Giuseppe Vizzielli, Stefano Restaino, Marco La Verde, Orazio De Tommasi, Marco Palumbo, Stefano Cianci
    Healthcare.2025; 13(6): 599.     CrossRef
  • Associations of the gut, cervical, and vaginal microbiota with cervical cancer: a systematic review and meta-analysis
    Qin Wen, Shubin Wang, Yalan Min, Xinyi Liu, Jian Fang, Jinyi Lang, Meihua Chen
    BMC Women's Health.2025;[Epub]     CrossRef
  • Quantification of Lactobacillus spp. of interest for the study of the vaginal microbiota
    Vivian Heimbecker, Bárbara Pontarollo Dal Santos, Ana Paula Thomaz, Keite da Silva Nogueira, Camila Marconi
    Journal of Microbiological Methods.2025; 236: 107158.     CrossRef
  • Associations of Atopobium, Garderella, Megasphaera, Prevotella, Sneathia, and Streptococcus with human papillomavirus infection, cervical intraepithelial neoplasia, and cancer: a systematic review and meta-analysis
    Yan Peng, Qin Tang, Shiming Wu, Chengzhi Zhao
    BMC Infectious Diseases.2025;[Epub]     CrossRef
  • Role of Vaginal and Gut Microbiota in Human Papillomavirus (HPV) Progression and Cervical Cancer: A Systematic Review of Microbial Diversity and Probiotic Interventions
    Hrishikesh D Pai, Rashmi Baid, Nandita P Palshetkar, Rishma Pai, Arnav Pai, Rohan Palshetkar
    Cureus.2025;[Epub]     CrossRef
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    Devanshi Gajjar, Sriram Seshadri
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    Angeliki Gerede, Konstantinos Nikolettos, Eleftherios Vavoulidis, Chrysoula Margioula-Siarkou, Stamatios Petousis, Maria Giourga, Panagiotis Fotinopoulos, Maria Salagianni, Sofoklis Stavros, Konstantinos Dinas, Nikolaos Nikolettos, Ekaterini Domali
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  • Advancements in the Vaginal Microenvironment and Regression of High-Risk Human Papillomavirus
    Na He, Cunjian Yi, Qingsong Zeng, Wumei Jing, Wenrong He
    Indian Journal of Microbiology.2024;[Epub]     CrossRef
  • Research Progress on Related Factors of Cervical High-Grade Squamous Intraepithelial Lesions
    红颖 王
    Advances in Clinical Medicine.2023; 13(12): 20536.     CrossRef
  • Role of the vaginal microbiome in miscarriage: exploring the relationship
    Marwa Saadaoui, Parul Singh, Osman Ortashi, Souhaila Al Khodor
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Reviews
Apoptotic Factors, CaNma111 and CaYbh3, Function in Candida albicans Filamentation by Regulating the Hyphal Suppressors, Nrg1 and Tup1
Suyoung Kim , Se Hyeon Kim , Eunjoong Kweon , Jinmi Kim
J. Microbiol. 2023;61(4):403-409.   Published online March 27, 2023
DOI: https://doi.org/10.1007/s12275-023-00034-8
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AbstractAbstract PDF
The morphological switch from the yeast to hyphal form is a key virulence attribute of the opportunistic fungal pathogen, Candida albicans. Our recent report showed that deletion of the newly identified apoptotic factor, CaNma111 or CaYbh3, leads to hyperfilamentation and increased virulence in a mouse infection model. CaNma111 and CaYbh3 are homologs of the pro-apoptotic protease, HtrA2/Omi, and BH3-only protein, respectively. In this study, we examined the effects of CaNMA111 and CaYBH3 deletion mutations on the expression levels of the hypha-specific transcr!ption factors, Cph1 (a hyphal activator), Nrg1 (a hyphal repressor), and Tup1 (a hyphal repressor). The protein levels of Nrg1 were decreased in Caybh3/Caybh3 cells while those of Tup1 were decreased in both Canma111/Canma111 and Caybh3/Caybh3 cells. These effects on Nrg1 and Tup1 proteins were retained during serum-induced filamentation and appear to explain the hyperfilamentation phenotypes of the CaNMA111 and CaYBH3 deletion mutants. Treatment with the apoptosis-inducing dose of farnesol decreased the Nrg1 protein levels in the wild-type strain and more evidently in Canma111/Canma111 and Caybh3/Caybh3 mutant strains. Together, our results suggest that CaNma111 and CaYbh3 are key regulators of Nrg1 and Tup1 protein levels in C. albicans.
Assembly of Bacterial Surface Glycopolymers as an Antibiotic Target
Hongbaek Cho
J. Microbiol. 2023;61(3):359-367.   Published online March 23, 2023
DOI: https://doi.org/10.1007/s12275-023-00032-w
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AbstractAbstract PDF
Bacterial cells are covered with various glycopolymers such as peptidoglycan (PG), lipopolysaccharides (LPS), teichoic acids, and capsules. Among these glycopolymers, PG assembly is the target of some of our most effective antibiotics, consistent with its essentiality and uniqueness to bacterial cells. Biosynthesis of other surface glycopolymers have also been acknowledged as potential targets for developing therapies to control bacterial infections, because of their importance for bacterial survival in the host environment. Moreover, biosynthesis of most surface glycopolymers are closely related to PG assembly because the same lipid carrier is shared for glycopolymer syntheses. In this review, I provide an overview of PG assembly and antibiotics that target this pathway. Then, I discuss the implications of a common lipid carrier being used for assembly of PG and other surface glycopolymers in antibiotic development.

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    Abdullah S. Alawam, Lina M. Alneghery, Maher S. Alwethaynani, Mubarak A. Alamri
    Journal of Biomolecular Structure and Dynamics.2025; 43(12): 6148.     CrossRef
  • Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development
    Jihyeon Min, Bitnara Kim, Yerim Park, Yongjun Son, Woojun Park
    Critical Reviews in Microbiology.2025; : 1.     CrossRef
  • Cross-linking teichoic acids by click chemistry prevents bacterial cell growth
    Morgane Baudoin, Anne Chouquet, Célia Boyat, Cédric Laguri, André Zapun, Basile Pérès, Cecile Morlot, Yung-Sing Wong, Claire Durmort
    Chemical Communications.2025; 61(54): 9940.     CrossRef
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    Ida K. S. Meitil, Garry P. Gippert, Kristian Barrett, Cameron J. Hunt, Bernard Henrissat
    Communications Biology.2024;[Epub]     CrossRef
  • Metalation of Extracytoplasmic Proteins and Bacterial Cell Envelope Homeostasis
    Bixi He, John D. Helmann
    Annual Review of Microbiology .2024; 78(1): 83.     CrossRef
  • Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
    Jin-Won Lee
    Journal of Microbiology.2023; 61(3): 273.     CrossRef
Journal Articles
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae , Hana Hyeon , Eunkyoung Shin , Ji&# , Kangseok Lee
J. Microbiol. 2023;61(2):211-220.   Published online February 22, 2023
DOI: https://doi.org/10.1007/s12275-023-00013-z
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AbstractAbstract PDF
RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity. Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication, at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the 5′-end (RNA I- 5) resulted in an approximately twofold increase in the steady-state levels of RNA I- 5 and the copy number of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These
results
indicate that RNA I- 5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5′-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5′-monophosphorylated end.

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  • Engineering an Escherichia coli based in vivo mRNA manufacturing platform
    Edward Curry, George Muir, Jixin Qu, Zoltán Kis, Martyn Hulley, Adam Brown
    Biotechnology and Bioengineering.2024; 121(6): 1912.     CrossRef
Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11
Wonsik Lee
J. Microbiol. 2022;60(12):1123-1129.   Published online November 24, 2022
DOI: https://doi.org/10.1007/s12275-022-2476-2
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AbstractAbstract PDF
Transposon mutant libraries are an important resource to study bacterial metabolism and pathogenesis. The fitness analysis of mutants in the libraries under various growth conditions provides important clues to study the physiology and biogenesis of structural components of a bacterial cell. A transposon library in conjunction with next-generation sequencing techniques, collectively named transposon sequencing (Tnseq), enables high-throughput genome profiling and synthetic lethality analysis. Tn-seq has also been used to identify essential genes and to study the mode of action of antibacterials. To construct a high-density transposon mutant library, an efficient delivery system for transposition in a model bacterium is essential. Here, I describe a detailed protocol for generating a high-density phage-based transposon mutant library in a Staphylococcus aureus strain, and this protocol is readily applicable to other S. aureus strains including USA300 and MW2.

Citations

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  • Optimizing phage-based mutant recovery and minimizing heat effect in the construction of transposon libraries in Staphylococcus aureus
    Sally W. Yousief, Nader Abdelmalek, Bianca Paglietti
    Scientific Reports.2024;[Epub]     CrossRef
Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6
Younkyung Choi , Minju Joo , Wooseok Song , Minho Lee , Hana Hyeon , Hyun-Lee Kim , Ji-Hyun Yeom , Kangseok Lee , Eunkyoung Shin
J. Microbiol. 2022;60(12):1162-1167.   Published online November 24, 2022
DOI: https://doi.org/10.1007/s12275-022-2437-9
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AbstractAbstract PDF
Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit ß peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.

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  • 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
  • Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
    Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
    Journal of Microbiology.2023; 61(2): 211.     CrossRef
Sulforaphane kills Mycobacterium tuberculosis H37Ra and Mycobacterium smegmatis mc2155 through a reactive oxygen species dependent mechanism
Yongjie Zhao , Shengwen Shang , Ya Song , Tianyue Li , Mingliang Han , Yuexuan Qin , Meili Wei , Jun Xi , Bikui Tang
J. Microbiol. 2022;60(11):1095-1105.   Published online September 1, 2022
DOI: https://doi.org/10.1007/s12275-022-2284-8
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AbstractAbstract PDF
Mycobacterium tuberculosis (M. tuberculosis) is a highly pathogenic intracellular pathogen that causes tuberculosis (TB), the leading cause of mortality from single infections. Redox homeostasis plays a very important role in the resistance of M. tuberculosis to antibiotic damage and various environmental stresses. The antioxidant sulforaphane (SFN) has been reported to exhibit anticancer activity and inhibit the growth of a variety of bacteria and fungi. Nonetheless, it remains unclear whether SFN exhibits anti-mycobacterial activity. Our
results
showed that the SFN against M. tuberculosis H37Ra exhibited bactericidal activity in a time and dose-dependent manner. The anti-tubercular activity of SFN was significantly correlated with bacterial reactive oxygen species (ROS) levels. In addition, SFN promoted the bactericidal effect of macrophages on intracellular bacteria in a dose-dependent manner, mediated by increasing intracellular mitochondrial ROS levels and decreasing cytoplasmic ROS levels. Taken together, our data revealed the previously unrecognized antimicrobial functions of SFN. Future studies focusing on the mechanism of SFN in macrophages against M. tuberculosis are essential for developing new host-directed therapeutic approaches against TB.

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    Fengqian Ma, Xuan Wang, Zhanghua Qiu, Shoupeng Ding, Wenya Du, Yumei Dai, Tao Ma, Linzhi Yue, Guofu Wang, Tao Wang, Ling Geng, Lixian Wu
    Cytokine.2024; 175: 156481.     CrossRef
  • Lactobacillus plantarum increase the sulforaphane formation efficiency via microbial-targeted delivery system in vivo
    Yunping Wang, Yiteng Zhang, Xiude Li, Liping Luo, Fangjian Ning, Tao Liu, Jinwang Li
    Food Bioscience.2024; 62: 105544.     CrossRef
  • Identifying autophagy-related genes as potential targets for immunotherapy in tuberculosis
    Sifang Xiao, Ting Zhou, Jianhua Pan, Xiaohua Ma, Guomin Shi, Binyuan Jiang, Yan-gen Xiang
    International Immunopharmacology.2023; 118: 109956.     CrossRef
Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt
Hye Seon Song , Juseok Kim , Yeon Bee Kim , Se Hee Lee , Tae Woong Whon , Seong Woon Roh
J. Microbiol. 2022;60(9):899-904.   Published online July 14, 2022
DOI: https://doi.org/10.1007/s12275-022-2137-5
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AbstractAbstract PDF
Two novel halophilic archaeal strains, CBA1133T and CBA- 1134, were isolated from solar salt in South Korea. The 16S rRNA gene sequences of the isolates were identical to each other and were closely related to the genera Natronomonas (92.3–93.5%), Salinirubellus (92.2%), Halomarina (91.3– 92.0%), and Haloglomus (91.4%). The isolated strains were coccoid, Gram-stain-negative, aerobic, oxidase-positive, and catalase-negative. Growth occurred under temperatures of 25–50°C (optimum, 45°C), NaCl levels of 10–30% (optimum, 15%), pH levels of 6.0–8.5 (optimum, 7.0), and MgCl2 concentrations of 0–500 mM (optimum, 100 mM). Digital DNADNA hybridization values between the strains and related genera ranged from 18.3% to 22.7%. The major polar lipids of the strains were phosphatidyl glycerol, phosphatidyl glycerol phosphate methyl ester, and phosphatidyl glycerol sulfate. Genomic, phenotypic, physiological, and biochemical analyses of the isolates revealed that they represent a novel genus and species in the family Halobacteriaceae. The type strain is CBA1133T (= KACC 22148T = JCM 34265T), for which the name Sala cibi gen. nov., sp. nov. is proposed.

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  • Dominance and diversity of archaea in food-grade salts: insights for histamine degradation in salt-fermented foods
    Jing Hou, Ya-Ling Mao, Na Li, Xiao-Yan Yang, Chidiebele Nwankwo, Heng-Lin Cui
    International Journal of Food Science and Technology.2024; 59(12): 9490.     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
  • Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat
    Yao Hu, Xue Ma, Shun Tan, Xin-Xin Li, Mu Cheng, Jing Hou, Heng-Lin Cui
    Antonie van Leeuwenhoek.2024;[Epub]     CrossRef
  • Assessing the impact of heavy metals on bacterial diversity in coastal regions of Southeastern India
    Chandra Veluchamy, Avinash Sharma, Kalaivani Thiagarajan
    Environmental Monitoring and Assessment.2024;[Epub]     CrossRef
  • Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
    Umakant Bhoopati Deshmukh, Aharon Oren
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Validation List no. 209. 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
  • Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt
    Ya-Ping Sun, Bei-Bei Wang, Zhang-Ping Wu, Xi-Wen Zheng, Jing Hou, Heng-Lin Cui
    Frontiers in Marine Science.2023;[Epub]     CrossRef
  • Naming new taxa of prokaryotes in the 21st century
    Aharon Oren
    Canadian Journal of Microbiology.2023; 69(4): 151.     CrossRef
Isolation of a novel Lactiplantibacillus plantarum strain resistant to nitrite stress and its transcriptome analysis
Chae Young Kwon , Kyoung Jin Choi , Dongeun Yong , Ji-Eun Kim , Sang Sun Yoon
J. Microbiol. 2022;60(7):715-726.   Published online July 4, 2022
DOI: https://doi.org/10.1007/s12275-022-2221-x
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AbstractAbstract PDF
Nitric oxide (NO) is a reactive nitrogen species (RNS) that plays a vital role in regulating inflammatory processes. Under abnormal conditions, excessive NO levels can promote the oxidation of cellular components, which may cause or exacerbate diseases such as hypertension, cardiovascular dysfunction, and inflammatory bowel disease (IBD). Previous studies have shown that reducing NO levels in the lumen can attenuate the clinical symptoms of IBD. Thus, we aimed to identify bacteria that can reduce RNS and that can be used as valuable probiotics. In this study, we isolated bacteria resistant to nitrite stress from human feces and used 16S and whole-genome sequencing to identify them as Lactiplantibacillus plantarum LP7 (LP7). The ability to survive at high nitrite levels and to decrease them was greater in the LP7 strain than in the reference strain L. plantarum ATCC14917 (ATCC- 14917). To characterize the LP7 genome in more detail, we performed a comparative genome analysis. However, the unique genes that directly confer the ability to withstand nitrite stress were not present in the LP7 genome. Furthermore, we performed transcriptomic analysis of LP7 and ATCC14917 cells treated with nitrite. We found that the expression levels of genes involved in the cell division process were induced in LP7, which showed a more regular rod-shape than ATCC- 14917. This could explain why LP7 can survive better than ATCC14917 under nitrite stress. Based on its ability to survive better in nitrite stress and decrease nitrite concentration, we suggest that LP7 could be a valuable probiotic strain.
Extracellular vesicles derived from Lactobacillus plantarum restore chemosensitivity through the PDK2-mediated glucose metabolic pathway in 5-FU-resistant colorectal cancer cells
JaeJin An , Eun-Mi Ha
J. Microbiol. 2022;60(7):735-745.   Published online July 4, 2022
DOI: https://doi.org/10.1007/s12275-022-2201-1
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  • 19 Crossref
AbstractAbstract PDF
Metabolic abnormalities are one of the main hallmarks of cancer and are associated with chemoresistance. Therefore, targeting the metabolic reprogramming of cancer cells has the potential to overcome chemoresistance. Probiotic-derived extracellular vesicles (EVs) play important roles in biological function and intracellular communication. However, the inhibitory effect of Lactobacillus plantarum-derived EVs (LpEVs) on colorectal cancer (CRC) cells has not yet been elucidated. This study clearly revealed that increased glycolysis in 5-fluorouracil (5-FU)-resistant CRC cells (CRC/5FUR) is directly related to chemoresistance and that the metabolic shift reversed by LpEVs inhibits cancer cell proliferation and eventually leads to apoptosis. Pyruvate dehydrogenase kinase 2 (PDK2), one of the crucial enzymes for enhancing glycolysis, was upregulated in CRC/5FUR cells. In our study, LpEVs sensitized CRC/5FUR cells to 5-FU by attenuating PDK2 expression in p53-p21-dependent metabolic signaling, thereby circumventing 5-FU resistance. We demonstrated the effect of cellular responses to 5-FU by modifying the PDK2 expression level in both 5-FU-sensitive parental CRC and 5- FU resistant CRC cell lines. Finally, we revealed that the PDK2 signaling pathway can potentially be targeted using LpEVs treatment to overcome chemoresistant CRC, thereby providing a potential strategy for CRC treatment by intervening in tumor metabolism.

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Gamma-glutamyltransferase of Helicobacter pylori alters the proliferation, migration, and pluripotency of mesenchymal stem cells by affecting metabolism and methylation status
Zeyu Wang , Weijun Wang , Huiying Shi , Lingjun Meng , Xin Jiang , Suya Pang , Mengke Fan , Rong Lin
J. Microbiol. 2022;60(6):627-639.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1575-4
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AbstractAbstract PDF
Virulence factor gamma-glutamyltransferase (GGT) of H. pylori consumes glutamine (Gln) in the stomach to decrease the tricarboxylic acid metabolite alpha-ketoglutarate (α-kg) and alter the downstream regulation of α-kg as well as cellular biological characteristics. Our previous research indicated that under H. pylori infection, mesenchymal stem cells (MSCs) migrated to the stomach and participated in gastric cancer (GC) development either by differentiating into epithelial cells or promoting angiogenesis. However, how MSCs themselves participate in H. pylori-indicated GC remains unclear. Therefore, a GGT knockout H. pylori strain (Hp- KS-1) was constructed, and downstream histone H3K9 and H3K27 methylation and the PI3K/AKT signaling pathway of α-kg were detected using Western blotting. The biological characteristics of MSCs were also examined. An additive α-kg supplement was also added to H. pylori-treated MSCs to investigate alterations in these aspects. Compared to the control and Hp-KS-1 groups, H. pylori-treated MSCs reduced Gln and α-kg, increased H3K9me3 and H3K27me3, activated the PI3K-AKT signaling pathway, and promoted the proliferation, migration, self-renewal, and pluripotency of MSCs. The addition of α-kg rescued the H. pylori-induced alterations. Injection of MSCs to nude mice resulted in the largest tumors in the H. pylori group and significantly reduced tumor sizes in the Hp-KS-1 and α-kg groups. In summary, GGT of H. pylori affected MSCs by interfering with the metabolite α-kg to increase trimethylation of histone H3K9 and H3K27, activating the PI3K/AKT signaling pathway, and promoting proliferation, migration, self-renewal, and pluripotency in tumorigenesis, elucidating the mechanisms of MSCs in GC development.

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  • Helicobacter pylori infection promotes the formation of the β‐catenin/HIF‐1α complex, enabling adaptive responses in gastric cancer cells
    Héctor A. Tapia, Camila García‐Navarrete, Patricio Silva, Joaquín Lizana, Carla Fonfach, Ignacio Pezoa‐Soto, Tania Flores, Nadia Hernández, Daniel Peña‐Oyarzún, Jorge Toledo, Safka Hernández‐Gutiérrez, Daniela Herrera, Manuel Varas‐Godoy, Denisse Bravo, V
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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
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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.

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    Chaofan Jiang, Lin Zhou, Mengke Wang, Sirui Shen, Weifeng Cheng, Qingchen Zhao, Kaidi Cui, Leiming He
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    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
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    Maeli Melotto, Brianna Fochs, Zachariah Jaramillo, Olivier Rodrigues
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    Libo Hou, Mengdi Wang, Hao Li, Lei Zhu, Xianghui Kong, Wei Gu, Keran Bi, Jie Du, Qingguo Meng
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Characterization of components of a reducing system for SoxR in the cytoplasmic membrane of Escherichia coli
Kang-Lok Lee , Kyung-Chang Lee , Joon-Hee Lee , Jung-Hye Roe
J. Microbiol. 2022;60(4):387-394.   Published online March 28, 2022
DOI: https://doi.org/10.1007/s12275-022-1667-1
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AbstractAbstract PDF
A reducing system of SoxR, a regulator of redox-active molecules, was identified as rsxABCDGE gene products and RseC in Escherichia coli through genetic studies. We found that ApbE was an additional component of the reducer system. Bacterial two hybrid analysis revealed that these proteins indeed had multiple interactions among themselves. RseC and RsxB formed the core of the complex, interacting with more than five other components. RsxC, the only cytoplasmic component of the system, interacted with SoxR. It might be linked with the rest of the complex via RsxB. Membrane fractions containing the wild type complex but not the mutant complex reduced purified SoxR using NADH as an electron source. These results suggest that Rsx genes, RseC, and ApbE can form a complex using NAD(P)H to reduce SoxR.

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  • The RNF/NQR redox pumps: a versatile system for energy transduction in bacteria and archaea
    Wolfgang Buckel, Ulrich Ermler, Janet Vonck, Günter Fritz, Julia Steuber
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    Rajdeep Banerjee, Erin L. Mettert, Angela S. Fleischhacker, Patricia J. Kiley
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    Julia Steuber, Günter Fritz
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  • Functional Characterization of RseC in the SoxR Reducing System and Its Role in Oxidative Stress Response in Escherichia coli
    Kang-Lok Lee, Joon-Hee Lee, Yun-Hee Kim, Jung-Hye Roe
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    Ruba Abdulrahman Ashy
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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
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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.

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  • 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
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    Hye-Young Kim, MubarakAli Davoodbasha, Jung-Wan Kim
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Changpingibacter yushuensis gen. nov., sp. nov., isolated from fluvial sediment in Qinghai Tibet Plateau of China
Yifan Jiao , Sihui Zhang , Jing Yang , Xin-He Lai , Kui Dong , Yanpeng Cheng , Mingchao Xu , Wentao Zhu , Shan Lu , Dong Jin , Ji Pu , Ying Huang , Liyun Liu , Suping Wang , Jianguo Xu
J. Microbiol. 2022;60(2):147-155.   Published online January 7, 2022
DOI: https://doi.org/10.1007/s12275-022-1199-8
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AbstractAbstract PDF
Two facultatively anaerobic, short rod-shaped, non-motile, Gram-stain-positive, unknown bacterial strains (JY-X040T and JY-X174) were isolated from fluvial sediments of Tongtian River in Yushu Tibetan Autonomous Prefecture, Qinghai province, China. Cells formed translucent, gray, round and convex colonies, with a diameter of less than 0.5 mm after 5 days of incubation at 30°C on brain heart infusion-5% sheep blood agar. The 16S rRNA gene sequence similarity between strain JY-X040T and Fudania jinshanensis 313T is 93.87%. In the four phylogenetic trees constructed based on the 16S rRNA gene and 423 core genes, the two isolates form an independent branch, phylogenetically closest to F. jinshanensis 313T, but could not be classified as a member of the genus Fudania or any other genus of the family Arcanobacteriaceae. The DNA G + C content of strain JY-X040T was 57.8%. Calculation
results
of average nucleotide identity, digital DNADNA hybridization value and amino acid identity between strain JY-X040T and F. jinshanensis 313T are 69.9%, 22.9%, and 64.1%. The major cellular fatty acids were C16:0 (23%) and C18:1ω9c (22%). The cell-wall peptidoglycan type was A5α (L-Lys-L-Ala-L-Lys-D-Glu). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and four unidentified components. The whole-cell sugars contained rhamnose and ribose. MK-10(H4) was the sole respiratory quinone. The minimum inhibitory concentration of streptomycin was 32 μg/ml. All physiological, biochemical, chemotaxonomic and genomic characteristics support that strains JY-X040T and JY-X174 represent members of a novel species in a new genus, Changpingibacter yushuensis gen. nov., sp. nov. The type strain is JY-X040T (GDMCC 1.1996T = KCTC 49514T).

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    Yi Yan, Jialiang Xu, Wenmin Huang, Yufeng Fan, Zhenpeng Li, Mingkai Tian, Jinsheng Ma, Xin Lu, Jian Liang
    Microorganisms.2024; 12(5): 911.     CrossRef
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    Maximilian Nepel, Veronika E. Mayer, Veronica Barrajon-Santos, Dagmar Woebken
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Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
Jaeyeong Park , Eunkyoung Shin , Ji-Hyun Yeom , Younkyung Choi , Minju Joo , Minho Lee , Je Hyeong Kim , Jeehyeon Bae , Kangseok Lee
J. Microbiol. 2022;60(1):128-136.   Published online December 29, 2021
DOI: https://doi.org/10.1007/s12275-022-1620-3
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AbstractAbstract PDF
Acinetobacter baumannii causes multidrug resistance, leading to fatal infections in humans. In this study, we showed that Lys AB2 P3-His–a hexahistidine-tagged form of an antimicrobial peptide (AMP) loaded onto DNA aptamer-functionalized gold nanoparticles (AuNP-Apt)–can effectively inhibit A. baumannii infection in mice. When A. baumannii-infected mice were intraperitoneally injected with AuNP-Apt loaded with Lys AB2 P3-His, a marked reduction in A. baumannii colonization was observed in the mouse organs, leading to prominently increased survival time and rate of the mice compared to those of the control mice treated with AuNP-Apt or Lys AB2 P3-His only. This study shows that AMPs loaded onto AuNP-Apt could be an effective therapeutic tool against infections caused by multidrug-resistant pathogenic bacteria in humans.

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    Seong Jin Choi, Eu Suk Kim
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    Md Minarul Islam, Da Eun Jung, Woo Shik Shin, Man Hwan Oh
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    Minho Lee
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    Sara M. Robledo, Silvia Pérez-Silanes, Celia Fernández-Rubio, Ana Poveda, Lianet Monzote, Víctor M. González, Paloma Alonso-Collado, Javier Carrión
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    Diandian Li, Yuan Su, Jie Li, Rong Liu, Bing Fang, Jingjing He, Wentao Xu, Longjiao Zhu
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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
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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.

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  • 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
Effect of exopolysaccharides of Paenibacillus polymyxa rhizobacteria on physiological and morphological variables of wheat seedlings
Irina V. Yegorenkova , Kristina V. Tregubova , Alexander I. Krasov , Nina V. Evseeva , Larisa Yu. Matora
J. Microbiol. 2021;59(8):729-735.   Published online July 24, 2021
DOI: https://doi.org/10.1007/s12275-021-0623-9
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AbstractAbstract PDF
Paenibacillus polymyxa is a promising plant-growth-promoting rhizobacterium that associates with a wide range of host plants, including agronomically important ones. Inoculation of wheat seedlings with P. polymyxa strains CCM 1465 and 92 was found to increase the mitotic index of the root cells 1.2- and 1.6-fold, respectively. Treatment of seedlings with the exopolysaccharides (EPSs) of these strains increased the mitotic index 1.9-fold (P. polymyxa CCM 1465) and 2.8-fold (P. polymyxa 92). These increases indicate activation of cell division in the root meristems. Analysis of the morphometric variables of the seedlings showed that P. polymyxa CCM 1465, P. polymyxa 92, and their EPSs promoted wheat growth, increasing root and shoot length up to 22% and root and shoot dry weight up to 28%, as compared with the control. In addition, both strains were found to intensely colonize the seedling root surface. Thus, P. polymyxa EPSs are active metabolites that, along with whole cells, are responsible for the contact interactions of the bacteria with wheat roots and are implicated in the induction of plant responses to these interactions. The strains used in this work are of interest for further study to broaden the existing understanding of the mechanisms of plant–bacterial interactions and to develop effective biofertilizers for agricultural purposes.

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  • Optimization of the Production Parameters of a Novel Exopolysaccharide Chrysosporine from Endophytic Chrysosporium sp. KTL2, and Evaluation of its Antioxidative and Prebiotic Potentialities
    Hiran Kanti Santra, Debdulal Banerjee
    Indian Journal of Microbiology.2025; 65(2): 1278.     CrossRef
  • Effect of a Bacillus velezensis and Lysinibacillus fusiformis-based biofertilizer on phosphorus acquisition and grain yield of soybean
    Luciana Cristina Vitorino, Elias José da Silva, Marilene Silva Oliveira, Isabella de Oliveira Silva, Lorraine da Silva Santos, Maria Andréia Corrêa Mendonça, Thais Cristina Sousa Oliveira, Layara Alexandre Bessa
    Frontiers in Plant Science.2024;[Epub]     CrossRef
  • Screening of Endophytic Antagonistic Bacteria in Wheat and Evaluation of Biocontrol Potential against Wheat Stripe Rust
    Ainisai Saimi, Qiqi Zhang, Qi Liu, Guangkuo Li, Haifeng Gao, Jing Chen
    Plants.2024; 13(10): 1366.     CrossRef
  • Basidiomycetes Polysaccharides Regulate Growth and Antioxidant Defense System in Wheat
    Olga Tsivileva, Andrei Shaternikov, Nina Evseeva
    International Journal of Molecular Sciences.2024; 25(13): 6877.     CrossRef
  • Exopolysaccharides of Paenibacillus polymyxa: A review
    Xuan-Ya Huang, Xin-Pei Ye, Yan-Yu Hu, Zhen-Xing Tang, Tian Zhang, Hai Zhou, Ting Zhou, Xue-Lian Bai, Er-Xu Pi, Bing-Hua Xie, Lu-E Shi
    International Journal of Biological Macromolecules.2024; 261: 129663.     CrossRef
  • Bacterial Inoculation and Co-Inoculation Improves Durum Wheat Productivity in Alkaline Calcareous Soils
    Souad Guemouri-Athmani, Bouazza Chami, Aurelio Scavo, Nabil Touzout, Djamel Baali-Cherif, Adil Mihoub, Jakub Černý, Muhammad Farhan Saeed, Aftab Jamal, Hayi Mohamed Yassine, Yaser Hassan Dewir
    Phyton.2024; 93(12): 3313.     CrossRef
  • Evaluation of Osmotolerant Potential of Halomonas sulfidaeris MV-19 Isolated from a Mud Volcano
    Ees Ahmad, Sushil K. Sharma, Abhijeet S. Kashyap, Nazia Manzar, Pramod K. Sahu, Udai B. Singh, Harsh V. Singh, Pawan K. Sharma
    Current Microbiology.2023;[Epub]     CrossRef
  • Watering Shapes a Robust and Stable Microbial Community under Fusarium Crown Rot Infection
    Runlai Xu, Chenghang Du, Yutian Gao, Xiaohan Zhou, Irsa Ejaz, Jieru Guo, Kunhu Chen, Jun Ma, Yinghua Zhang, Zhimin Wang, Zhencai Sun
    Agronomy.2023; 13(5): 1356.     CrossRef
  • Biological activity of silver nanoparticles synthesized with Paenibacillus polymyxa exopolysaccharides
    Kristina V. Tregubova, Irina V. Yegorenkova, Vyacheslav S. Grinev, Alexander S. Fomin
    Enzyme and Microbial Technology.2023; 164: 110174.     CrossRef
  • Optimizing the Growth Conditions of the Selected Plant-Growth-Promoting Rhizobacteria Paenibacillus sp. MVY-024 for Industrial Scale Production
    Justina Kaziūnienė, Raimonda Mažylytė, Aurimas Krasauskas, Monika Toleikienė, Audrius Gegeckas
    Biology.2022; 11(5): 745.     CrossRef
  • Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1
    Pascal Mülner, Elisa Schwarz, Kristin Dietel, Stefanie Herfort, Jennifer Jähne, Peter Lasch, Tomislav Cernava, Gabriele Berg, Joachim Vater
    Pathogens.2021; 10(11): 1485.     CrossRef
Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China
Ju-Wei Wang , Pei-Jie Han , Da-Yong Han , Sen Zhou , Kuan Li , Peng-Yu He , Pan Zhen , Hui-Xin Yu , Zhen-Rong Liang , Xue-Wei Wang , Feng-Yan Bai
J. Microbiol. 2021;59(8):753-762.   Published online July 5, 2021
DOI: https://doi.org/10.1007/s12275-021-1115-7
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AbstractAbstract PDF
The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55–18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85–23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.

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  • Saccharomycopsis yichangensis sp. nov., a Novel Predacious Yeast Species Isolated From Soil
    Shuang Hu, Liang‐Chen Guo, Yan‐Jie Qiu, Qi‐Yang Zhu, Ri‐Peng Zhang, Pei‐Jie Han, Feng‐Yan Bai
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    Jingsha Zhao, Xiangying Qin, Qinxuan Yuan, Shiwei Wang, Changtao Wang, Dongdong Wang, Jiachan Zhang, Meng Li
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    Zelong Zhong, Tianyi Liu, Kaiping He, Min Zhong, Xiaoxue Chen, Yansong Xue, Beizhong Han, Diqiang Wang, Jun Liu
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  • Exploring the heterogeneity of community and function and correspondence of “species-enzymes” among three types of Daqu with different fermentation peak-temperature via high-throughput sequencing and metagenomics
    Ying Huang, Dong Li, Yu Mu, Zhiyu Zhu, Yuzhang Wu, Qi Qi, Yingchun Mu, Wei Su
    Food Research International.2024; 176: 113805.     CrossRef
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    Jiamu Kang, Xiaoning Huang, Rengshu Li, Yuandi Zhang, Xiao-Xue Chen, Bei-Zhong Han
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    Qi Yu, Feiyan Mou, Junwen Xiao, Cheng Zhan, Liang Li, Xu Chang, Xiaoyuan Dong, Maobin Chen, Xinrui Wang, Mei Chen, Shangling Fang
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
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    Hongmei Yin, Qiang Hong, Xiang Yu, Hui Wang, Xiaodan Shi, Wei Liu, Tao Yuan, Zongcai Tu
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    Boyang Xu, Shanshan Xu, Hao Zhou, Ruijuan Wang, Chao Jiang, Dongdong Mu, Xuefeng Wu, Xiaolei Wu, Shaotong Jiang, Xingjiang Li
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    Yuanyuan Pan, Ying Wang, Wenjun Hao, Sen Zhou, Chengbao Duan, Qiushi Li, Jinwang Wei, Gang Liu
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    Yanbo Liu, Haideng Li, Shumei Dong, Zhou Zhou, Zhenke Zhang, Runna Huang, Suna Han, Jianguang Hou, Chunmei Pan
    LWT.2023; 173: 114290.     CrossRef
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    Qi Zhu, Liangqiang Chen, Zheng Peng, Qiaoling Zhang, Wanqiu Huang, Fan Yang, Guocheng Du, Juan Zhang, Li Wang
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    Pei-Jie Han, Lu-Jun Luo, Ying Han, Liang Song, Pan Zhen, Da-Yong Han, Yu-Hua Wei, Xin Zhou, Zhang Wen, Jun-Zhi Qiu, Feng-Yan Bai
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    Jiamu Kang, Liangliang Jia, Zhongxiao Zhang, Min Zhang, Xiaoning Huang, Xiaoxue Chen, Bei-Zhong Han
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    Jiao Niu, Shiqi Yang, Yi Shen, Wei Cheng, Hehe Li, Jinyuan Sun, Mingquan Huang, Baoguo Sun
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    Jiamu Kang, Xiaoxue Chen, Bei-Zhong Han, Yansong Xue
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Deep convolutional neural network: a novel approach for the detection of Aspergillus fungi via stereomicroscopy
Haozhong Ma , Jinshan Yang , Xiaolu Chen , Xinyu Jiang , Yimin Su , Shanlei Qiao , Guowei Zhong
J. Microbiol. 2021;59(6):563-572.   Published online March 29, 2021
DOI: https://doi.org/10.1007/s12275-021-1013-z
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AbstractAbstract PDF
Fungi of the genus Aspergillus are ubiquitously distributed in nature, and some cause invasive aspergillosis (IA) infections in immunosuppressed individuals and contamination in agricultural products. Because microscopic observation and molecular detection of Aspergillus species represent the most operator-dependent and time-intensive activities, automated and cost-effective approaches are needed. To address this challenge, a deep convolutional neural network (CNN) was used to investigate the ability to classify various Aspergillus species. Using a dissecting microscopy (DM)/stereomicroscopy platform, colonies on plates were scanned with a 35× objective, generating images of sufficient resolution for classification. A total of 8,995 original colony images from seven Aspergillus species cultured in enrichment medium were gathered and autocut to generate 17,142 image crops as training and test datasets containing the typical representative morphology of conidiophores or colonies of each strain. Encouragingly, the Xception model exhibited a classification accuracy of 99.8% on the training image set. After training, our CNN model achieved a classification accuracy of 99.7% on the test image set. Based on the Xception performance during training and testing, this classification algorithm was further applied to recognize and validate a new set of raw images of these strains, showing a detection accuracy of 98.2%. Thus, our study demonstrated a novel concept for an artificial-intelligence-based and cost-effective detection
method
ology for Aspergillus organisms, which also has the potential to improve the public’s understanding of the fungal kingdom.

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  • Superficial Fungal Infections and Artificial Intelligence: A Review on Current Advances and Opportunities: REVISION
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    Oscar J. Suarez, Daniel C. Ruiz-Ayala, Liliana Rojas Contreras, Manuel G. Forero, Jesús A. Medrano-Hermosillo, Abraham Efraim Rodriguez-Mata
    Agriculture.2025; 15(17): 1888.     CrossRef
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Role of melatonin in murine “restraint stress”-induced dysfunction of colonic microbiota
Rutao Lin , Zixu Wang , Jing Cao , Ting Gao , Yulan Dong , Yaoxing Chen
J. Microbiol. 2021;59(5):500-512.   Published online February 25, 2021
DOI: https://doi.org/10.1007/s12275-021-0305-7
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AbstractAbstract PDF
Intestinal diseases caused by physiological stress have become a severe public health threat worldwide. Disturbances in the gut microbiota-host relationship have been associated with irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory and antioxidant effects. The objective of this study was to investigate the mechanisms by which MT-mediated protection mitigated stress-induced intestinal microbiota dysbiosis and inflammation. We successfully established a murine restraint stress model with and without MT supplementation. Mice subjected to restraint stress had significantly elevated corticosterone (CORT) levels, decreased MT levels in their plasma, elevated colonic ROS levels and increased bacterial abundance, including Bacteroides and Tyzzerella, in their colon tract, which led to elevated expression of Toll-like receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation with 20 mg/kg MT reversed the elevation of the plasma CORT levels, downregulated the colon ROS levels and inhibited the changes in the intestinal microbiota induced by restraint stress. These effects, in turn, inhibited the activities of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory reaction induced by restraint stress. Our results suggested that MT may mitigate “restraint stress”-induced colonic microbiota dysbiosis and intestinal inflammation by inhibiting the activation of the NF-κB pathway.

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  • Impact of Sex, Gonadectomy, and Repeated Restraint Stress on Gut Microbiome in Mice
    Chahrazed Mekadim, Jakub Mrázek, Martin Vodička, Peter Ergang, Kateřina Olša Fliegerová, Tiziana Maria Mahayri, Kallayanee Chawengsaksophak, Jiří Pácha
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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
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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.

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    Eunsil Choi, Ahhyun Huh, Changmin Oh, Jeong-Il Oh, Ho Young Kang, Jihwan Hwang
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Caspase-3 inhibitor inhibits enterovirus D68 production
Wenbo Huo , Jinghua Yu , Chunyu Liu , Ting Wu , Yue Wang , Xiangling Meng , Fengmei Song , Shuxia Zhang , Ying Su , Yumeng Liu , Jinming Liu , Xiaoyan Yu , Shucheng Hua
J. Microbiol. 2020;58(9):812-820.   Published online September 1, 2020
DOI: https://doi.org/10.1007/s12275-020-0241-y
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AbstractAbstract PDF
Enterovirus D68 (EVD68) is an emerging pathogen that recently caused a large worldwide outbreak of severe respiratory disease in children. However, the relationship between EVD68 and host cells remains unclear. Caspases are involved in cell death, immune response, and even viral production. We found that caspase-3 was activated during EVD68 replication to induce apoptosis. Caspase-3 inhibitor (Z-DEVDFMK) inhibited viral production, protected host cells from the cytopathic effects of EVD68 infection, and prevented EVD68 from regulating the host cell cycle at G0/G1. Meanwhile, caspase-3 activator (PAC-1) increased EVD68 production. EVD68 infection therefore activates caspase-3 for virus production. This knowledge provides a potential direction for the prevention and treatment of disease related to EVD68.

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Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri Vent Field of the Central Indian Ocean ridge
Jae Kyu Lim , Yun Jae Kim , Jhung-Ahn Yang , Teddy Namirimu , Sung-Hyun Yang , Mi-Jeong Park , Yong Min Kwon , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon
J. Microbiol. 2020;58(4):260-267.   Published online April 1, 2020
DOI: https://doi.org/10.1007/s12275-020-9424-9
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AbstractAbstract PDF
A strictly anaerobic, dissimilatory Fe(III)-reducing hyperthermophilic archaeon, designated as strain IOH1T, was isolated from a new deep-sea hydrothermal vent (Onnuri Vent Field) area in the Central Indian Ocean ridge. Strain IOH1T showed > 99% 16S rRNA gene sequence similarity with Thermococcus celericrescens TS2T (99.4%) and T. siculi DSM 12349T (99.2%). Additional three species T. barossii SHCK-94T (99.0%), T. celer Vu13T (98.8%), and T. piezophilus (98.6%) showed > 98.6% of 16S rRNA gene sequence similarity, however, the maximum OrthoANI value is 89.8% for the genome of T. celericrescens TS2T. Strain IOH1T cells are coccoid, 1.2–1.8 μm in diameter, and motile by flagella. Growth was at 70–82°C (optimum 80°C), pH 5.4–8.0 (optimum pH 6.0) with 2–4% (optimum 3%) NaCl. Growth of strain IOH1T was enhanced by starch, pyruvate, D(+)-maltose and maltodextrin as a carbon sources, and elemental sulfur as an electron acceptor; clearly different from those of related species T. celecrescens DSM 17994T and T. siculi DSM 12349T. Strain IOH1T, T. celercrescence DSM 17994T, and T. siculi DSM 12349T reduced soluble Fe(III)-citrate present in the medium, whereas the amount of total cellular proteins increased with the concomitant accumulation of Fe(II). We determined a circular chromosome of 2,234 kb with an extra-chromosomal archaeal plasmid, pTI1, of 7.7 kb and predicted 2,425 genes. The DNA G + C content was 54.9 mol%. Based on physiological properties, phylogenetic, and genome analysis, we proposed that strain IOH1T (= KCTC 15844T = JCM 39077T) is assigned to a new species in the genus Thermococcus and named Thermococcus indicus sp. nov.

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Natronorubrum halophilum sp. nov. isolated from two inland salt lakes
Cong-Qi Tao , Yi Ding , Yang-Jie Zhao , Heng-Lin Cui
J. Microbiol. 2020;58(2):105-112.   Published online January 29, 2020
DOI: https://doi.org/10.1007/s12275-020-9514-8
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AbstractAbstract PDF
Two halophilic archaeal strains, SHR37T and NEN6, were isolated from salt lakes located in the Tibet and Xinjiang regions of China. The two strains were found to form a single cluster (99.9% and 99.3% similarity, respectively) separating them from the six current members of Natronorubrum (94.7– 96.9% and 86.1–90.8% similarity, respectively) on the basis of the 16S rRNA and rpoB􍿁 gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains SHR37T and NEN6 from current Natronorubrum members. Their polar lipids are C20C20 and C20C25 glycerol diether derivatives of PG, PGP-Me, and a major glycolipid chromatographically identical to disulfated mannosyl glucosyl diether (S2-DGD). Four minor unidentified glycolipids are also present. The OrthoANI and in silico DDH values of the two strains were 97.3% and 76.1%, respectively, which were much higher than the threshold values proposed as a species boundary (ANI 95–96% and in silico DDH 70%), which revealed that the two strains represent one species; the two values (ANI 79.0–81.9% and in silico DDH 23.5– 25.7%) of the strains examined in this study and the current members of Natronorubrum are much lower than the recommended threshold values, suggesting that strains SHR37T and NEN6 represent a genomically different species of Natronorubrum. These results showed that strains SHR37T (= CGMCC 1.15233T = JCM 30845T) and NEN6 (= CGMCC 1.17161) represent a novel species of Natronorubrum, for which the name Natronorubrum halophilum sp. nov. is proposed.

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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
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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).

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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
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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).

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  • 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
Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter
Soo-Jin Kim , Hayoung Cho , Jae-Hyung Ahn , Hang-Yeon Weon , Jae-Ho Joa , Jeong-Seon Kim , Soon-Wo Kwon
J. Microbiol. 2019;57(10):836-841.   Published online June 27, 2019
DOI: https://doi.org/10.1007/s12275-019-9118-3
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AbstractAbstract PDF
A Gram-stain-positive, rod-shaped, non-endospore-forming, motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4–35°C (optimum, 28–30°C), pH 5.0–9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

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    Louise Vermote, Byung Hee Chun, Shehzad Abid Khan, Luc De Vuyst, Che Ok Jeon, Stefan Weckx
    International Journal of Food Microbiology.2025; 440: 111283.     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
  • Makgeolli - The Traditional Choice of Korean Fermented Beverage from Cereal: An Overview on its Composition and Health Benefits
    Ganesh SHIMOGA, Sang-Youn KIM
    Food Science and Technology.2022;[Epub]     CrossRef
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    Chi Zhao, Wei Su, Yu Mu, Yingchun Mu, Li Jiang
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  • 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
Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean
Libo Yu , Xixiang Tang , Shiping Wei , Yinkun Qiu , Xiashutong Xu , Guangxin Xu , Qilin Wang , Qian Yang
J. Microbiol. 2019;57(7):562-568.   Published online June 27, 2019
DOI: https://doi.org/10.1007/s12275-019-8709-3
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AbstractAbstract PDF
A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15–50°C (optimum 37°C), pH 5–10.5 (optimum 7), 0–5% NaCl (optimum 1%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03T was a member of the genus Lysinibacillus. Strain YLB-03T was closely related to Lysinibacillus sinduriensis BLB-1T and Lysinibacillus chungkukjangi 2RL3-2T (98.4%), Lysinibacillus halotolerans LAM- 612T (98.0%), Lysinibacillus telephonicus KT735049T (97.5%), Lysinibacillus endophyticus C9T (97.5%), Lysinibacillus composti NCCP-36T and Lysinibacillus massiliensis 4400831T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03T and closely related type strains were 73.7–76.3% and 34.7–38.7%, respectively. The principal fatty acids were anteiso-C15:0 and iso-C15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03T (= MCCC 1A12698T = JCM 32871T).

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  • Genomic, bioinformatics, and functional analysis of a novel bioremediation bacterial strain from mangrove sediment
    Khadije Ahmad Amin, Gihan Daw Elbait, Ahmed F. Yousef, Habiba Al Safar, Syed Salman Ashraf
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    Joyce Amarachi Aja, Lawrence Dave Llorin, Kenji Rowel Q. Lim, Jade Joshua Teodosio, Erwin John Sioson, Ron L. Dy, Carlo A. Arcilla, Doralyn S. Dalisay, Jose Enrico Hizon Lazaro
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  • Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. nov.
    Amit Yadav, Ruchi Teware, Agrima Bhatt, Yash Bhavsar, Akanksha Maurya, Vipool Thorat, Venkata Ramana Vemuluri, Kiran Kirdat
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    Hiyu Kanbe, Yuki Sano, Kazumori Mise, Shusei Kanie, Natsumi Ushijima, Keisuke Kawano, Minoru Kihara, Hideomi Itoh
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    Xinxu Zhang, Zongbao Liu, Wei Xu, Jie Pan, Yuhan Huang, Mingwei Cai, Zhuhua Luo, Meng Li
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Screening and identification of Aspergillus activity against Xanthomonas oryzae pv. oryzae and analysis of antimicrobial components
Bei Jiang , Zhiying Wang , Chuxuan Xu , Weijia Liu , Donghua Jiang
J. Microbiol. 2019;57(7):597-605.   Published online June 27, 2019
DOI: https://doi.org/10.1007/s12275-019-8330-5
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AbstractAbstract PDF
To screen for Aspergillus activity against Xanthomonas oryzae pv. oryzae and analyse the antimicrobial components involved, 60 Aspergillus spp. were isolated and purified from fruits, soil and other habitats. As-75, an Aspergillus strain that can antagonize Xanthomonas oryzae pv. oryzae, was identified based on the zone of inhibition formed during co-culture. According to morphological, ITS rDNA gene sequencing and phylogenetic tree results, the strain showed close homology to Aspergillus sclerotiorum. The biochemical characterization tests showed that the fermentation broth of strain As-75 exhibited a high capacity for environmental adaptation. The results of the antimicrobial spectrum experiments demonstrated that As-75 exhibited fairly strong antagonistic activity against five plant pathogenic fungi and six plant pathogenic bacteria in vitro. The fermentation broth of strain As-75 displayed maximum stability under fluorescent illumination at temperatures below 60°C at pH 6.5. A substance with antagonistic activity was obtained from strain As-75 via fractional extraction, silica gel column chromatography and thinlayer chromatography. Through mass spectrometry, nuclear magnetic resonance and electrospray ionization mass spectrometry (ESI-MS) analyses, the target compound was identified as (2Z)-2-butenedioic acid-2-(1-methylethenyl)-4-methyl ester; its molecular weight of 170.06 daltons and formula of C8H10O4 identify it as a novel compound. Trials of the preventative and curative effects demonstrated that compound S1 exhibited a better control efficiency than the control against rice bacterial blight. Additionally, the M1 processing
method
was better, and the efficiency of compound S1 in preventing rice bacterial blight in six rice varieties, TN1, IR24, ZF802, Zhonghua 11, Wuyunjing 21, and Nipponbare, was 78.3%, 77.5%, 74.2%, 75.3%, 70.9%, and 72.1%, respectively.

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    Suyan Wang, Yanxia Wang, Xinchi Shi, Daniela D. Herrera-Balandrano, Xin Chen, Fengquan Liu, Pedro Laborda, Irina S. Druzhinina
    Applied and Environmental Microbiology.2024;[Epub]     CrossRef
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    Ming Fang, Jie Sun, Ailing Wang, Hongbo Tang, Lei Wang, Xianqin Wei, Weibin Ruan
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    Yanjie Yi, Shijie Liu, Shihao Ren, Yunpeng Shen, Xinyue Lin, Jia Shi, Kang Wang, Changfu Zhang
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    Xuan-Dong WANG, Sun-Yu-Yue YANG, Run-Jie GAO, Jun-Jie YU, Dan-Pei ZHENG, Feng NI, Dong-Hua JIANG
    Acta Agronomica Sinica.2022; 48(6): 1546.     CrossRef
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    Huaixiang Tian, Yao Liu, Li Li, Chen Chen, Haiyan Yu, Xinxin Ma, Juan Huang, Xinman Lou, Haibin Yuan
    Food Bioscience.2022; 50: 101988.     CrossRef
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    Yanjie Yi, Yang Liu, Pengyu Luan, Zhipeng Hou, Yanhui Yang, Ruifang Li, Zhenpu Liang, Xiaoxia Zhang, Shulei Liu
    Egyptian Journal of Biological Pest Control.2022;[Epub]     CrossRef
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    Biological Control.2022; 176: 105066.     CrossRef
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    Xudong Ouyang, Jelmer Hoeksma, Gisela van der Velden, Wouter A. G. Beenker, Maria H. van Triest, Boudewijn M. T. Burgering, Jeroen den Hertog
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Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula
Hyeon-Woo Koh , Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Hongik Kim , Soo-Je Park
J. Microbiol. 2019;57(9):732-737.   Published online May 11, 2019
DOI: https://doi.org/10.1007/s12275-019-8540-x
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AbstractAbstract PDF
A Gram-stain-positive, oxidase- and catalase-positive, motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5T was observed at 15–37°C (optimum 30°C) on R2A broth, pH 6.0–8.0 (optimum 7.0), and 0–5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5T was most closely related to Arthrobacter silviterrae KIS14-16T, Arthrobacter livingstonensis LI2T, Arthrobacter stackebrandtii CCM 2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5T was 64.7 mol%, and its DNA–DNA relatedness values with A. silviterrae KIS14-16T, A. livingstonensis LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus GP3T, A. ramosus CCM 1646T, and A. cryoconiti Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H2) and major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5T (= KCTC 49189T = LMG 31284T).

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    Atif Khurshid Wani, Nahid Akhtar, Farooq Sher, Acacio Aparecido Navarrete, Juliana Heloisa Pinê Américo-Pinheiro
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  • Arthrobacter sunyaminii sp. nov. and Arthrobacter jiangjiafuii sp. nov., new members in the genus Arthrobacter
    Gui Zhang, Jing Yang, Dong Jin, Xin-He Lai, Shan Lu, Zhihong Ren, Tian Qin, Liyun Liu, Ji Pu, Yue Liu, Lin Ye, Juan Zhou, Xianglian Lv, Yuanmeihui Tao, Jianguo Xu
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  • Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions
    Sara Gushgari-Doyle, Lauren M Lui, Torben N Nielsen, Xiaoqin Wu, Ria G Malana, Andrew J Hendrickson, Heloise Carion, Farris L Poole, Michael W W Adams, Adam P Arkin, Romy Chakraborty
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Identification and characterization of a marine-derived chitinolytic fungus, Acremonium sp. YS2-2
Dawoon Chung , Kyunghwa Baek , Seung Seob Bae , Jaejoon Jung
J. Microbiol. 2019;57(5):372-380.   Published online February 26, 2019
DOI: https://doi.org/10.1007/s12275-019-8469-0
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AbstractAbstract PDF
Chitin is the most abundant biopolymer in marine environments. To facilitate its utilization, our laboratory screened marine-derived fungal strains for chitinolytic activity. One chitinolytic strain isolated from seawater, designated YS2-2, was identified as Acremonium species based on morphological and phylogenetic analyses. Acremonium species are cosmopolitan fungi commonly isolated from both terrestrial and marine environments, but their chitinolytic activity is largely unknown. The extracellular crude enzyme of YS2-2 exhibited optimum chitinolytic activity at pH 6.0–7.6, 23–45°C, and 1.5% (w/v) NaCl. Degenerate PCR revealed the partial cDNA sequence of a putative chitinase gene, chiA, in YS2-2. The expression of chiA was dramatically induced in response to 1% (w/v) colloidal chitin compared to levels under starvation, chitin powder, and glucose conditions. Moreover, the chiA transcript levels were positively correlated with chitinolytic activities under various colloidal chitin concentrations, suggesting that ChiA mediates chitinolytic activity in this strain. Our results provide a basis for additional studies of marinederived chitinolytic fungi aimed at improving industrial applications.

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Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine
Ji-Sun Kim , Hanna Choe , Yu-Ri Lee , Kyung Mo Kim , Doo-Sang Park
J. Microbiol. 2019;57(5):381-387.   Published online February 22, 2019
DOI: https://doi.org/10.1007/s12275-019-8631-8
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AbstractAbstract PDF
A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102T was most closely related to Kandleria vitulina DSM 20405T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053T (91.1%), Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis DSM 5348T (89.6%). The average nucleotide identity values between strain SG0102T and related species, K. vitulina DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G+C content of the strain SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2 ω9/12c. The cell wall peptidoglycan of strain SG0102T contained the meso-diaminopimelic acid. The strain SG0102T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102T (= KCTC 15725T = NBRC 113396T).

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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
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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).

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Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces
Ji-Sun Kim , Keun Chul Lee , Min Kuk Suh , Kook-Il Han , Mi Kyung Eom , Ju Huck Lee , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Byeong Seob Oh , Seung Yeob Yu , Seung-Hyeon Choi , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Seung-Jo Yang , Jung-Sook Lee
J. Microbiol. 2019;57(1):38-44.   Published online December 29, 2018
DOI: https://doi.org/10.1007/s12275-019-8550-8
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AbstractAbstract PDF
A Gram-stain-positive, obligately anaerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).

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Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula
Man-Young Jung , Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Soo-Je Park
J. Microbiol. 2019;57(2):107-112.   Published online November 19, 2018
DOI: https://doi.org/10.1007/s12275-019-8500-5
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AbstractAbstract PDF
The novel Gram-stain-negative, rod-shaped, aerobic bacterial strain DCR-13T was isolated from a native plant belonging to the genus Campanula on Dokdo, an island in the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence indicated that this strain is closely related to Paraburkholderia peleae PP52-1T (98.43% 16S rRNA gene sequence similarity), Paraburkholderia oxyphila NBRC 105797T (98.42%), Paraburkholderia sacchari IPT 101T (98.28%), Paraburkholderia mimosarum NBRC 106338T (97.80%), Paraburkholderia denitrificans KIS30-44T (97.46%), and Paraburkholderia paradise WAT (97.45%). This analysis of the 16S rRNA gene sequence also suggested that DCR-13T and the six closely related strains formed a clade within the genus Paraburkholderia, but that DCR-13T was clearly separated from the established species. DCR-13T had ubiquinone 8 as its predominant respiratory quinone, and its genomic DNA G + C content was 63.9 mol%. The isolated strain grew at a pH of 6.0–8.0 (with an optimal pH of 6.5), 0–4% w/v NaCl (with an optimal level of 0%), and a temperature of 18–42°C (with an optimal temperature of 30°C). The predominant fatty acids were C16:0, summed feature 8 (C18:1 ω7c/C18:1 ω6c), C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1 ω6c/C16:1 ω7c) and summed feature 2 (C12:0 aldehyde), and the major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. On the basis of polyphasic evidence, it is proposed that strain DCR-13T (= KCTC 62811T = LMG 30889T) represents the type strain of a novel species, Paraburkholderia dokdonella sp. nov.

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Gramella fulva sp. nov., isolated from a dry surface of tidal flat
Sae Hyun Hwang , Woon Mo Hwang , Keunsoo Kang , Tae-Young Ahn
J. Microbiol. 2019;57(1):23-29.   Published online November 19, 2018
DOI: https://doi.org/10.1007/s12275-019-8370-x
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AbstractAbstract PDF
A novel Gram-stain-negative, aerobic, motile by means of gliding, and short rod-shaped bacterium, designated strain SH35T, was isolated from the dry surface of a tidal flat in Hwasung-si, South Korea. Growth occurred at 10–40°C (optimum 30°C), at pH 6.0–8.0 (optimum pH 7.0), in 1–12% NaCl (optimum 2%), and was inhibited in the absence of NaCl and Ca2+ ions. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH35T belonged to the genus Gramella and was a member of the family Flavobacteriaceae with highest sequence similarity to Gramella flava JLT2011T (96.1%), followed by Gramella oceani CCAMSZ- TT (95.6%), and 93.0–94.9% to other recognized Gramella species. The major cellular fatty acids (> 5% of the total) of strain SH35T were iso-C15:0, Iso-C16:0, anteiso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or C17:1 iso ω9с). The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and nine unidentified polar lipids. The major respiratory quinone and the predominant polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content was 40.5 mol% (39.7% based on total genome calculations). Based on phylogenetic analysis and physiological and biochemical characterization, strain SH35T represents a novel species of the genus Gramella, for which the name Gramella fulva sp. nov. is proposed. The type strain is SH35T (= KACC 19447T = JCM 32369T).

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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
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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).

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