Journal of Microbiology

Full article

Whole-genome characterization and global phylogenetic comparison of cefotaxime-resistant Escherichia coli isolated from broiler chickens: Shahana Ahmed, Tridip Das, Chandan Nath, Tahia Ahmed, Keya Ghosh, Pangkaj Kumar Dhar, Ana Herrero-Fresno, Himel Barua, Paritosh Kumar Biswas, Md Zohorul Islam, John Elmerdahl Olsen; J. Microbiol. 2025;63(4):e2412009. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2412009

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Abstract PDF Supplementary Material: Antimicrobial resistance (AMR) poses a serious threat to public health, with the emergence of extended-spectrum beta-lactamases (ESBLs) in Enterobacteriaceae, particularly Escherichia coli, raising significant concerns. This study aims to elucidate the drivers of antimicrobial resistance, and the global spread of cefotaxime-resistant E. coli (CREC) strains. Whole-genome sequencing (WGS) was performed to explore genome-level characteristics, and phylogenetic analysis was conducted to compare twenty CREC strains from this study, which were isolated from broiler chicken farms in Bangladesh, with a global collection (n = 456) of CREC strains from multiple countries and hosts. The MIC analysis showed over 70% of strains isolated from broiler chickens exhibiting MIC values ≥ 256 mg/L for cefotaxime. Notably, 85% of the studied farms (17/20) tested positive for CREC by the end of the production cycle, with CREC counts increasing from 0.83 ± 1.75 log10 CFU/g feces on day 1 to 5.24 ± 0.72 log10 CFU/g feces by day 28. WGS revealed the presence of multiple resistance genes, including bla_CTX-M, which was found in 30% of the strains. Phylogenetic comparison showed that the Bangladeshi strains were closely related to strains from diverse geographical regions and host species. This study provides a comprehensive understanding of the molecular epidemiology of CREC. The close phylogenetic relationships between Bangladeshi and global strains demonstrate the widespread presence of cefotaxime-resistant bacteria and emphasize the importance of monitoring AMR in food-producing animals to mitigate the spread of resistant strains.

Research Article

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia: Eunju Hong, Youngjin Shin, Hyunseong Kim, Woo Young Cho, Woo-Hyun Song, Seung-Hyun Jung, Minho Lee; J. Microbiol. 2025;63(1):e.2409020. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409020

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Abstract PDF Supplementary Material: With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Journal Article

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Abstract

Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

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From Farm to Community: Dispersal of Potentially Pathogenic Staphylococcus and Mammaliicoccus Species and Antimicrobial Resistance Across Shared Environments
Faizan Ahmad, Samuel Sathler Martuchelle, Ana Luisa Andrade-Oliveira, Vitor Emanuel Lanes Viana, Maria Antônia Silva Melo Sousa, Felipe Sicchierolli da Silveira, Marisa Alves Nogueira-Diaz, Monalessa Fábia Pereira, Marcia Giambiagi-deMarval, Ciro César Ro
Current Microbiology.2025;[Epub] CrossRef
Genomic insights into multidrug and heavy metal resistance in Chryseobacterium sp. BI5 isolated from sewage sludge
Mrinmoy Patra, Anand Kumar Pandey, Suresh Kumar Dubey
Total Environment Microbiology.2025; 1(1): 100005. CrossRef

Reviews

Balancing Act of the Intestinal Antimicrobial Proteins on Gut Microbiota and Health: Ye Eun Ra, Ye‑Ji Bang; J. Microbiol. 2024;62(3):167-179. Published online April 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00122-3

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Abstract

The human gut houses a diverse and dynamic microbiome critical for digestion, metabolism, and immune development, exerting profound efects on human health. However, these microorganisms pose a potential threat by breaching the gut barrier, entering host tissues, and triggering infections, uncontrolled infammation, and even sepsis. The intestinal epithelial cells form the primary defense, acting as a frontline barrier against microbial invasion. Antimicrobial proteins (AMPs), produced by these cells, serve as innate immune efectors that regulate the gut microbiome by directly killing or inhibiting microbes. Abnormal AMP production, whether insufcient or excessive, can disturb the microbiome equilibrium, contributing to various intestinal diseases. This review delves into the complex interactions between AMPs and the gut microbiota and sheds light on the role of AMPs in governing host-microbiota interactions. We discuss the function and mechanisms of action of AMPs, their regulation by the gut microbiota, microbial evasion strategies, and the consequences of AMP dysregulation in disease. Understanding these complex interactions between AMPs and the gut microbiota is crucial for developing strategies to enhance immune responses and combat infections within the gut microbiota. Ongoing research continues to uncover novel aspects of this intricate relationship, deepening our understanding of the factors shaping gut health. This knowledge has the potential to revolutionize therapeutic interventions, ofering enhanced treatments for a wide range of gut-related diseases.

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Host-directed therapies modulating innate immunity against infection in hematologic malignancies
Qiong Wang, Kristján Hermannsson, Egill Másson, Peter Bergman, Guðmundur Hrafn Guðmundsson
Blood Reviews.2025; 70: 101255. CrossRef
Progress in the Identification and Design of Novel Antimicrobial Peptides Against Pathogenic Microorganisms
Shengwei Sun
Probiotics and Antimicrobial Proteins.2025; 17(2): 918. CrossRef
Comparison of naturalization mouse model setups uncover distinct effects on intestinal mucosa depending on microbial experience
Henriette Arnesen, Signe Birkeland, Harriet Stendahl, Klaus Neuhaus, David Masopust, Preben Boysen, Harald Carlsen
Discovery Immunology.2025;[Epub] CrossRef
Oral administration of LEAP2 enhances immunity against Edwardsiella tarda through regulation of gut bacterial community and metabolite in mudskipper
Ting-Fang Zhu, Hai-Peng Guo, Li Nie, Jiong Chen
Fish & Shellfish Immunology.2025; 158: 110128. CrossRef
Pharmacology of Intestinal Inflammation and Repair
Céline Deraison, Nathalie Vergnolle
Annual Review of Pharmacology and Toxicology .2025; 65(1): 301. CrossRef
Macrophages and Gut Barrier Function: Guardians of Gastrointestinal Health in Post-Inflammatory and Post-Infection Responses
Edward Xiangtai Meng, George Nicholas Verne, Qiqi Zhou
International Journal of Molecular Sciences.2024; 25(17): 9422. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
Gut Microbiota as Emerging Players in the Development of Alcohol-Related Liver Disease
Wei Li, Wenkang Gao, Shengqi Yan, Ling Yang, Qingjing Zhu, Huikuan Chu
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Membrane Proteins as a Regulator for Antibiotic Persistence in Gram‑Negative Bacteria: Jia Xin Yee , Juhyun Kim , Jinki Yeom; J. Microbiol. 2023;61(3):331-341. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00024-w

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Abstract

Antibiotic treatment failure threatens our ability to control bacterial infections that can cause chronic diseases. Persister bacteria are a subpopulation of physiological variants that becomes highly tolerant to antibiotics. Membrane proteins play crucial roles in all living organisms to regulate cellular physiology. Although a diverse membrane component involved in persistence can result in antibiotic treatment failure, the regulations of antibiotic persistence by membrane proteins has not been fully understood. In this review, we summarize the recent advances in our understanding with regards to membrane proteins in Gram-negative bacteria as a regulator for antibiotic persistence, highlighting various physiological mechanisms in bacteria.

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Amino Acid and Au(III) Self-Assembled Supramolecular Nanozymes for Antimicrobial Applications
Yunzhu Xu, Dahai Hou, Min Zhao, Tong Zhao, Yong Ma, Yafeng Zhang, Yang Guo, Weiwei Tao, Hui Wang
ACS Applied Nano Materials.2024; 7(19): 22505. CrossRef
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
mSystems.2024;[Epub] 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

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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Abstract

The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

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Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production
Lufeng Chen, Guoyi Cheng, Zhengwen Zhou, Yong Liang, Zhijia Ci, Yongguang Yin, Guangliang Liu, Yong Cai, Yanbin Li
Water Research.2024; 258: 121792. CrossRef
Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef
Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples
Agata Anna Cisek, Iwona Bąk, Bożena Cukrowska
Microorganisms.2023; 11(3): 660. CrossRef

Incomplete autophagy promotes the replication of Mycoplasma hyopneumoniae: Zhaodi Wang† , Yukang Wen† , Bingqian Zhou , Yaqin Tian , Yaru Ning , Honglei Ding; J. Microbiol. 2021;59(8):782-792. Published online July 5, 2021; DOI: https://doi.org/10.1007/s12275-021-1232-3

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Abstract

Autophagy is an important cellular homeostatic mechanism for recycling of degradative proteins and damaged organelles. Autophagy has been shown to play an important role in cellular responses to bacteria and bacterial replication. However, the role of autophagy in Mycoplasma hyopneumoniae infection and the pathogenic mechanism is not well characterized. In this study, we showed that M. hyopneumoniae infection significantly increases the number of autophagic vacuoles in host cells. Further, we found significantly enhanced expressions of autophagy marker proteins (LC3-II, ATG5, and Beclin 1) in M. hyopneumoniae-infected cells. Moreover, immunofluorescence analysis showed colocalization of P97 protein with LC3 during M. hyopneumoniae infection. Interestingly, autophagic flux marker, p62, accumulated with the induction of infection. Conversely, the levels of p62 and LC3-II were decreased after treatment with 3-MA, inhibiting the formation of autophagosomes, during infection. In addition, accumulation of autophagosomes promoted the expression of P97 protein and the survival of M. hyopneumoniae in PK- 15 cells, as the replication of M. hyopneumoniae was downregulated by adding 3-MA. Collectively, these findings provide strong evidence that M. hyopneumoniae induces incomplete autophagy, which in turn enhances its reproduction in host cells. These findings provide novel insights into the interaction of M. hyopneumoniae and host.

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Research Progress on Immune Evasion of Mycoplasma hyopneumoniae
Bin Jiang, Ying Zhang, Gaojian Li, Yanping Quan, Jianhong Shu, Huapeng Feng, Yulong He
Microorganisms.2024; 12(7): 1439. CrossRef
The Role of Pyroptosis and Autophagy in Ischemia Reperfusion Injury
Huijie Zhao, Yihan Yang, Xinya Si, Huiyang Liu, Honggang Wang
Biomolecules.2022; 12(7): 1010. CrossRef
Mycoplasma bovis inhibits autophagy in bovine mammary epithelial cells via a PTEN/PI3K-Akt-mTOR-dependent pathway
Maolin Xu, Yang Liu, Tuerdi Mayinuer, Yushan Lin, Yue Wang, Jian Gao, Dong Wang, John P. Kastelic, Bo Han
Frontiers in Microbiology.2022;[Epub] CrossRef
Incomplete autophagy promotes the proliferation of Mycoplasma hyopneumoniae through the JNK and Akt pathways in porcine alveolar macrophages
Yukang Wen, Zhengkun Chen, Yaqin Tian, Mei Yang, Qingshuang Dong, Yujiao Yang, Honglei Ding
Veterinary Research.2022;[Epub] CrossRef

The putative sensor histidine kinase VadJ coordinates development and sterigmatocystin production in Aspergillus nidulans: Yanxia Zhao , Mi-Kyung Lee , Jieyin Lim , Heungyun Moon , Hee-Soo Park , Weifa Zheng , Jae-Hyuk Yu; J. Microbiol. 2021;59(8):746-752. Published online July 5, 2021; DOI: https://doi.org/10.1007/s12275-021-1055-2

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Abstract

The VosA-VelB heterocomplex governs expression of several genes associated with fungal development and secondary metabolism. In this study, we have investigated the functions of one of the VosA-VelB-activated developmental genes vadJ in development and production of the mycotoxin sterigmatocystin in the model fungus Aspergillus nidulans. The vadJ gene is predicted to encode a 957-amino acid length protein containing a highly conserved sensor histidine kinase domain. The deletion of vosA or velB resulted in decreased mRNA levels of vadJ throughout the life cycle, suggesting that VosA and VelB are necessary for proper expression of vadJ. Nullifying vadJ led to highly restricted colony growth, lowered formation of asexual spores, and about two-fold reduction in conidial viability. Conversely, the deletion of vadJ resulted in elevated production of sexual fruiting bodies and sterigmatocystin. These suggest that VadJ is necessary for proper coordination of asexual and sexual development, and sterigmatocystin production. In accordance with this idea, the deletion of vadJ led to elevated mRNA levels of the two key sexual developmental activators esdC and nsdD. In summary, the putative sensor histidine kinase VadJ represses sexual development and sterigmatocystin production, but activates asexual development in A. nidulans.

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Velvet Family Protein FpVelB Affects Virulence in Association with Secondary Metabolism in Fusarium pseudograminearum
Yuxing Wu, Sen Han, Yajiao Wang, Qiusheng Li, Lingxiao Kong
Cells.2024; 13(11): 950. CrossRef
Involvement of LaeA and Velvet Proteins in Regulating the Production of Mycotoxins and Other Fungal Secondary Metabolites
Xuwen Hou, Liyao Liu, Dan Xu, Daowan Lai, Ligang Zhou
Journal of Fungi.2024; 10(8): 561. CrossRef
Adaptative responses of Neurospora crassa by histidine kinases upon the attack of the arthropod Sinella curviseta
Ting Lu, Xiao-meng Wang, Peng-xu Chen, Juan Xi, Han-bing Yang, Wei-fa Zheng, Yan-xia Zhao
Current Genetics.2024;[Epub] CrossRef
Implication of VelB in the development, pathogenicity, and secondary metabolism of Penicillium expansum
Nadia Tahtah, Chrystian Zetina-Serrano, Ophélie Rocher, Claire Naylies, Yannick Lippi, André El Khoury, Ali Atoui, Emilien L. Jamin, Isabelle P. Oswald, Sophie Lorber, Olivier Puel
Postharvest Biology and Technology.2023; 195: 112121. CrossRef
Regulators of the Asexual Life Cycle of Aspergillus nidulans
Ye-Eun Son, Jae-Hyuk Yu, Hee-Soo Park
Cells.2023; 12(11): 1544. CrossRef
Post‐translational modifications drive secondary metabolite biosynthesis in Aspergillus: a review
Kunlong Yang, Jun Tian, Nancy P. Keller
Environmental Microbiology.2022; 24(7): 2857. CrossRef
The Putative C2H2 Transcription Factor VadH Governs Development, Osmotic Stress Response, and Sterigmatocystin Production in Aspergillus nidulans
Xiaoyu Li, Yanxia Zhao, Heungyun Moon, Jieyin Lim, Hee-Soo Park, Zhiqiang Liu, Jae-Hyuk Yu
Cells.2022; 11(24): 3998. CrossRef

Type 2 human papillomavirus E7 attenuates E-cadherin expression in human keratinocytes: Ji Young Song , Young Min Park , Soon Yong Choi; J. Microbiol. 2021;59(6):616-625. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0690-y

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Abstract

Human papillomaviruses (HPVs) are known to utilize the down-regulation of epithelial (E)-cadherin, a major component of adherens junctions of keratinocytes, to evade host immune surveillance in high-risk group. However, the effects of HPV on the function of E-cadherin in low-risk groups remain unknown. We investigated whether type 2 HPV (HPV- 2) E7 could induce alterations in E-cadherin expression in transiently transfected keratinocytes and cell lines expressing HPV-2 E7. To examine the expression pattern of E-cadherin in cutaneous warts and normal skin samples, immunohistochemical analysis was performed. Quantitative real-time polymerase chain reactions, luciferase assays, western blot, immunocytochemistry, and electron microscopy were used to evaluate the mRNA and protein expression levels of Ecadherin in normal human epidermal keratinocytes transfected with HPV-2 E7 plasmid DNA or E7-specific siRNA and in E7-expressing cell lines. E-cadherin expression levels in HPV-2 positive cutaneous warts were significantly decreased compared to those in normal skin (p < 0.05). Similarly, the mRNA and protein expression levels of E-cadherin in E7 transiently transfected cells were significantly decreased compared to those in empty vector-transfected cells. The decreases were restored by transfection with E7-specific siRNA (p < 0.05). Likewise, cell lines expressing E7 showed a decreased expression of E-cadherin. When the cells were cultured in low attachment plates, cell-to-cell aggregation was inhibited. Taken together, our data suggest that HPV-2 E7, the causative agent of cutaneous warts, could mediate the transcriptional repression of E-cadherin.

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The NLRP3 inflammasome in viral infection (Review)
Qiaoli Zheng, Chunting Hua, Qichang Liang, Hao Cheng
Molecular Medicine Reports.2023;[Epub] CrossRef

Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus: Dong-Wook Hyun , Euon Jung Tak , Pil Soo Kim , Jin-Woo Bae; J. Microbiol. 2021;59(2):132-141. Published online December 23, 2020; DOI: https://doi.org/10.1007/s12275-021-0485-1

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Abstract

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17AT and HDW17BT, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolates were members of the genus Vagococcus, and strain HDW17AT was closely related to Vagococcus fessus CCUG 41755T (98.9% of 16S rRNA gene sequence similarity and 74.3% of average nucleotide identity [ANI]), whereas strain HDW17BT was closely related to Vagococcus fluvialis NCFB 2497T (98.9% of 16S rRNA gene sequence similarity and 76.6% of ANI). Both strains contained C16:0, and C18:1 ω9c as the major cellular fatty acids, but C16:1 ω9c was also observed only in strain HDW17BT as the major cellular fatty acid. The respiratory quinone of the isolates was MK-7. The major polar lipid components were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The genomic DNA G + C content of strains HDW17AT and HDW17BT were 36.6 and 34.4%, respectively. Both strains had cell wall peptidoglycan composed of the amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan, L-lysine, and L-aspartic acid, and the sugars ribose, glucose, and galactose. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW17AT and HDW17BT represent two novel species in the genus Vagococcus. We propose the name Vagococcus coleopterorum sp. nov. for strain HDW17AT (= KACC 21348T = KCTC 49324T = JCM 33674T) and the name Vagococcus hydrophili sp. nov. for strain HDW17BT (= KACC 21349T = KCTC 49325T = JCM 33675T).

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Vagococcus proximus sp. nov. and Vagococcus intermedius sp. nov., originating from modified atmosphere packaged broiler meat
Per Johansson, Elina Jääskeläinen, Elina Säde, Johanna Björkroth
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
A case of Vagococcus fluvialis isolated from the bile of a patient with calculous cholecystitis
Dan Zhang, Xiaosu Wang, Jingdan Yu, Zheng Dai, Qichao Li, Litao Zhang
BMC Infectious Diseases.2023;[Epub] CrossRef
Vagococcus luciliae sp. nov., isolated from the common green bottle fly Lucilia sericata
Juan Guzman, Anja Poehlein, Rolf Daniel, Peter Kämpfer, Andreas Vilcinskas
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
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Huijuan Pan, Qi Yu, Chenru Qian, Haitao Shao, Jiajun Han, Yongyong Li, Yongjiang Lou
Food Bioscience.2021; 42: 101198. CrossRef
Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)
Dong-Wook Hyun, Yun-Seok Jeong, Jae-Yun Lee, Hojun Sung, So-Yeon Lee, Jee-Won Choi, Hyun Sik Kim, Pil Soo Kim, Jin-Woo Bae
Journal of Microbiology.2021; 59(6): 552. CrossRef

Characterization of a novel dsRNA mycovirus of Trichoderma atroviride NFCF377 reveals a member of “Fusagraviridae” with changes in antifungal activity of the host fungus: Jeesun Chun , Byeonghak Na , Dae-Hyuk Kim; J. Microbiol. 2020;58(12):1046-1053. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0380-1

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Abstract

Trichoderma atroviride is a common fungus found in various ecosystems that shows mycoparasitic ability on other fungi. A novel dsRNA virus was isolated from T. atroviride NFCF377 strain and its molecular features were analyzed. The viral genome consists of a single segmented double-stranded RNA and is 9,584 bp in length, with two discontinuous open reading frames (ORF1 and ORF2). A mycoviral structural protein and an RNA-dependent RNA polymerase (RdRp) are encoded by ORF1 and ORF2, respectively, between which is found a canonical shifty heptameric signal motif (AAAAAAC) followed by an RNA pseudoknot. Analysis of sequence similarity and phylogeny showed that it is closely related to members of the proposed family “Fusagraviridae”, with a highest similarity to the Trichoderma atroviride mycovirus 1 (TaMV1). Although the sequence similarity of deduced amino acid to TaMV1 was evident, sequence deviations were distinctive at untranslated regions (UTRs) due to the extended size. Thus, we inferred this dsRNA to be a different strain of Trichoderma atroviride mycovirus 1 (TaMV1-NFCF377). Electron microscopy image exhibited an icosahedral viral particle of 40 nm diameter. Virus-cured isogenic isolates were generated and no differences in growth rate, colony morphology, or conidia production were observed between virus-infected and virus-cured strains. However, culture filtrates of TaMV1- NFCF377-infected strain showed enhanced antifungal activity against the plant pathogen Rhizoctonia solani but not to edible mushroom Pleurotus ostreatus. These results suggested that TaMV1-NFCF377 affected the metabolism of the fungal host to potentiate antifungal compounds against a plant pathogen, but this enhanced antifungal activity appeared to be species-specific.

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Co-infection with two novel mycoviruses affects the biocontrol activity of Trichoderma polysporum
Jeesun Chun, Hae-Ryeong Yoon, Sei-Jin Lee, Dae-Hyuk Kim
Biological Control.2024; 188: 105440. CrossRef
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Chenchen Liu, Xiliang Jiang, Zhaoyan Tan, Rongqun Wang, Qiaoxia Shang, Hongrui Li, Shujin Xu, Miguel A. Aranda, Beilei Wu, Lea Atanasova
Microbiology Spectrum.2023;[Epub] CrossRef
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Siwei Li, Zhihao Ma, Xinyi Zhang, Yibo Cai, Chenggui Han, Xuehong Wu
Journal of Fungi.2023; 10(1): 30. CrossRef
Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture
Miriam Schalamun, Monika Schmoll
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Subha Das, Sakae Hisano, Ana Eusebio-Cope, Hideki Kondo, Nobuhiro Suzuki
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Mark R. McNeill, Xiongbing Tu, Eric Altermann, Wu Beilei, Shengjing Shi
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Carolina Cornejo, Sakae Hisano, Helena Bragança, Nobuhiro Suzuki, Daniel Rigling
Journal of Fungi.2021; 7(10): 861. CrossRef

Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina: Kah-Ooi Chua , Wah-Seng See-Too , Jia-Yi Tan , Sze-Looi Song , Hoi-Sen Yong , Wai-Fong Yin , Kok-Gan Chan; J. Microbiol. 2020;58(12):988-997. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0325-8

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Abstract

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1 ω7c, C16:0, C19:0 ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteraceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

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Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kämpfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Mizue Anda, Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda, Wataru Iwasaki
Nature Communications.2023;[Epub] CrossRef
Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina
Kah-Ooi Chua, Yvonne Jing Mei Liew, Wah-Seng See-Too, Jia-Yi Tan, Hoi-Sen Yong, Wai-Fong Yin, Kok-Gan Chan
Antonie van Leeuwenhoek.2022; 115(8): 995. CrossRef
Pharmacological potential of ants and their symbionts – a review
Surbhi Agarwal, Garima Sharma, Kavita Verma, Narayanan Latha, Vartika Mathur
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Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
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Stenotrophomonas maltophilia outer membrane protein A induces epithelial cell apoptosis via mitochondrial pathways: Xin Wang , Yan Li , Xueping Tang , Xueyi Shang , Zunquan Zhao , Yongqiang Jiang , Yan Li; J. Microbiol. 2020;58(10):868-877. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0235-9

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Abstract

Stenotrophomonas maltophilia (S. maltophilia) is a common opportunistic pathogen in intensive care units and causes infections most often after surgeries in immune-compromised patients such as those undergoing chemotherapy. Outer membrane protein A (OmpA) is the most abundant of the outer membrane proteins in S. maltophilia. Previous studies on OmpA usually focus on its interaction with the host cells and its role in vaccine development. However, the impact of OmpA on the virulence of S. maltophilia to host cells and the effects on apoptosis remain unclear. In this study, we exposed purified recombinant S. maltophilia OmpA (rOmpA) to HEp-2 cells and investigated the effects of OmpA on epithelial cell apoptosis. Morphologic and flow cytometric analyses revealed that HEp-2 cells stimulated with rOmpA multiple apoptosis features, including nuclear roundness and pyknosis, chromatin aggregation, and phosphatidylserine eversion. We found that rOmpA regulated the protein levels of Bax and Bcl-xL in HEp-2 cells, leading to changes in mitochondria permeability and the release of cytochrome c and apoptosis-inducing factors into the cytoplasm. These subsequently activate the caspase-9/caspase-3 pathway that promote apoptosis. We also observed that rOmpA enhanced the generation of reactive oxygen species and increased intracellular Ca2+ levels in HEp-2 cells. Collectively, our data suggested that rOmpA induced epithelial cells apoptosis via mitochondrial pathways.

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Functional analysis of OmpA and its contribution to pathogenesis of Edwardsiella tarda
Quan Zhou, Yushuai Hu, Yicheng You, Yingli Gao, Xingqiang Wang, Lei Qin
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Xiaoyan Xu, Tianhao Zhou, Xudong Wei, Xuelian Jiang, Jiyan Cao
Drug Delivery.2023;[Epub] CrossRef
Control of host mitochondria by bacterial pathogens
Saverio Marchi, Gianluca Morroni, Paolo Pinton, Lorenzo Galluzzi
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Limiting the pathogenesis of Salmonella Typhimurium with berry phenolic extracts and linoleic acid overproducing Lactobacillus casei: Zajeba Tabashsum , Mengfei Peng , Cassendra Bernhardt , Puja Patel , Michael Carrion , Shaik O. Rahaman , Debabrata Biswas; J. Microbiol. 2020;58(6):489-498. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-9545-1

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Abstract

The growing threat of emergent multidrug-resistant enteric bacterial pathogens, and their adopted virulence properties are directing to find alternative antimicrobials and/or development of dietaries that can improve host gut health and/or defense. Recently, we found that modified Lactobacillus casei (Lc + CLA) with increased production of conjugated linoleic acid has antimicrobial and other beneficial properties. Further, prebiotic alike products such as berry pomace extracts (BPEs), increase the growth of probiotics and inhibit the growth of certain bacterial pathogens. In this study, we evaluated the antibacterial effect of genetically modified Lc + CLA along with BPEs against major enteric pathogen Salmonella enterica serovar Typhimurium (ST). In mixed culture condition, the growth of ST was significantly reduced in the presence of Lc + CLA and/or BPEs. Bacterial cell-free cultural supernatant (CFCS) collected from wild-type Lc or modified Lc + CLA strains also inhibited the growth and survival of ST, and those inhibitory effects were enhanced in the presence of BPEs. We also found that the interaction of the pathogen with cultured host (HD-11 and INT-407) cells were also altered in the presence of either Lc or Lc + CLA strain or their CFCSs significantly. Furthermore, the relative expression of genes related to ST virulence and physicochemical properties of ST was altered by the effect of CFCSs of either Lc or Lc + CLA. These findings indicate that a diet containing synbiotic, specifically linoleic acid, over-produced Lc + CLA and prebiotic product BPEs, might have the potential to be effective in controlling ST growth and pathogenesis.

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Natural anti-adhesive components against pathogenic bacterial adhesion and infection in gastrointestinal tract: case studies of Helicobacter pylori , Salmonella enterica , Clostridiu
Xiaoyu Bao, Jianping Wu
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Zajeba Tabashsum, Zabdiel Alvarado‐Martinez, Matthew J. Wall, Arpita Aditya, Debabrata Biswas
Journal of Food Science.2023; 88(6): 2583. CrossRef
Intracellular autolytic whole cell Salmonella vaccine prevents colonization of pathogenic Salmonella Typhimurium in chicken
Mengfei Peng, Jungsoo Joo, Zabdiel Alvarado-Martinez, Zajeba Tabashsum, Arpita Aditya, Debabrata Biswas
Vaccine.2022; 40(47): 6880. CrossRef
Lactobacilli, a Weapon to Counteract Pathogens through the Inhibition of Their Virulence Factors
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Florfenicol Enhances Colonization of a Salmonella enterica Serovar Enteritidis floR Mutant with Major Alterations to the Intestinal Microbiota and Metabolome in Neonatal Chickens
Xueran Mei, Boheng Ma, Xiwen Zhai, Anyun Zhang, Changwei Lei, Lei Zuo, Xin Yang, Changyu Zhou, Hongning Wang, Johanna Björkroth
Applied and Environmental Microbiology.2021;[Epub] CrossRef

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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Abstract

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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