Article
Microbiology
Sayyad Ali Raza Bukhari, Muhammad Irfan, Irfan Ahmad, Lijing Chen
Summary: This study is important as it provides a refined pan-genome profile of A. muciniphila by excluding too-diverse strains. It also elucidates the horizontal gene transfer and recombination patterns, and performs a comparative evaluation of the metabolic potential.
Article
Biochemistry & Molecular Biology
Cheng-Kuo Lai, Yi-Chien Lee, Huei-Mien Ke, Min R. Lu, Wei-An Liu, Hsin-Han Lee, Yu-Ching Liu, Toyoshi Yoshiga, Taisei Kikuchi, Peichen J. Chen, Isheng Jason Tsai
Summary: In this study, the genomes of six Aphelenchoides species, including four strains of the A. besseyi species complex, were analyzed. The systematic identification of horizontal gene transfer (HGT) genes revealed that these genes were mostly acquired from bacteria, fungi, and plants. This study provides a comprehensive understanding of HGT in nematodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Microbiology
Liangzhi Li, Zhenghua Liu, Zhicheng Zhou, Min Zhang, Delong Meng, Xueduan Liu, Ye Huang, Xiutong Li, Zhen Jiang, Shuiping Zhong, Lukasz Drewniak, Zhendong Yang, Qian Li, Yongjun Liu, Xiaolong Nan, Biguang Jiang, Chengying Jiang, Huaqun Yin
Summary: This study provides an in-depth exploration of the diversity, metabolic potential, and genetic evolution of the DPANN archaeal superphylum, revealing differences among them and the role of lateral gene transfer in shaping their genetic flexibility.
Article
Biochemistry & Molecular Biology
Iago Rodrigues Blanco, Lucas Jose Luduverio Pizauro, Joao Victor dos Anjos Almeida, Carlos Miguel Nobrega Mendonca, Alessandro de Mello Varani, Ricardo Pinheiro de Souza Oliveira
Summary: This study compared the genomes of P. pentosaceus available in the public GenBank database, focusing on their pediocin-like bacteriocin repertoire. The analysis revealed a temporal signal in the pattern of gene gain and loss, indicating that the complete genetic repertoire of this bacterial group is still unknown. Thirteen bacteriocin genes from Class II and III were predicted, and four pediocin-like bacteriocins and their accompanying immunity genes were highlighted. In silico modeling showed differences in the helix motif compared to physically determined pediocin-like structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Microbiology
Xiaobin Gu, Xiuhai Lu, Shudan Lin, Xinrui Shi, Yue Shen, Qingsong Lu, Yiying Yang, Jing Yang, Jiabei Cai, Chunyan Fu, Yongliang Lou, Meiqin Zheng
Summary: This study identified horizontal gene transfer events between Acanthamoeba and amoeba-resisting microorganisms, shedding light on the pathogenic mechanisms of diseases.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Yvonne O. Ogaji, Robert C. Lee, Tim I. Sawbridge, Benjamin G. Cocks, Hans D. Daetwyler, Sukhjiwan Kaur
Summary: This study used Oxford Nanopore long-read sequencing to generate high-quality genome and mitochondrial genome assemblies for 18 isolates of the Australian Ascochyta Blight (AB) complex, revealing differences and similarities between the pathogens. It was found that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic.
Article
Genetics & Heredity
Victoria Mesa, Marc Monot, Laurent Ferraris, Michel Popoff, Christelle Mazuet, Frederic Barbut, Johanne Delannoy, Bruno Dupuy, Marie-Jose Butel, Julio Aires
Summary: This study provides the closed genome assembly and functional annotation of Clostridium neonatale ATCC BAA-265(T) reference strain. Pan-genome, core-genome, and accessory genome analyses reveal the genetic diversity and plasticity of C. neonatale genomes. The findings contribute to the understanding of the biological capabilities of this species.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Lior Glick, Itay Mayrose
Summary: The study of intraspecific genomic variation in eukaryotic species has been a focus of recent genome resequencing projects, with the use of the pan-genome concept presenting advantages over reference-based methods. However, constructing pan-genomes for eukaryotic species remains a challenging task, requiring tailored analysis pipelines and hindering research reproducibility and comparison. The software package Panoramic aims to simplify pan-genome construction for eukaryotic species by providing a user-friendly interface and efficient data processing algorithms.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemical Research Methods
Qihua Liang, Stefano Lonardi
Summary: PGV is a reference-agnostic representation of a species' pan-genome based on consensus ordering, enabling intuitive, effective, and interactive visualization of complex structural genomic variations. The PGV software can be easily installed via conda or downloaded from the website, with a companion browser available for testing using example bed tracks from the GitHub page.
BMC BIOINFORMATICS
(2021)
Article
Microbiology
Jie Xu, Chen Mei, Yan Zhi, Zhi-Xuan Liang, Xue Zhang, Hong-Jun Wang
Summary: This study compared the genomic characteristics of A. paragallinarum OMVs with its parent strain and investigated the transfer of ARGs via OMVs. The results showed that ARGs delivered by OMVs were transiently present on antibiotic-containing plates, but lost by the second bacterial passage.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Carlos Caicedo-Montoya, Monserrat Manzo-Ruiz, Rigoberto Rios-Estepa
Summary: This study utilized 121 genome sequences of the genus Streptomyces to estimate genomic diversity and identify potential antibiotic gene clusters. The open pan-genome of Streptomyces was observed, with a high quantity of unique gene families across species. Phylogenetic relationships were described using multiple markers, and 33 biosynthetic gene clusters with antibiotic potential were identified.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Xudong Liu, Zhinan Wu, Tongyuan Hu, Xiaoqian Lin, Hewei Liang, Wenxi Li, Xin Jin, Liang Xiao, Xiaodong Fang, Yuanqiang Zou
Summary: This study provides new insights into the genomic diversity analysis of L. acidophilus and uncovers the ecological adaptation of specific strains.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Food Science & Technology
Rui Luo, Chen Liu, Yu Li, Qing Liu, Xin Su, Qingting Peng, Xueyan Lei, Weicheng Li, Bilige Menghe, Qiuhua Bao, Wenjun Liu
Summary: In this study, whole genome sequencing analysis of multiple strains of L. kefiranofaciens was conducted, revealing the genomic characteristics and evolutionary process of this species. Differences in functional genes and bacteriocins were observed among the strains, which were associated with the isolation habitat.
Article
Plant Sciences
Jianshuang Shen, Xueqin Li, Mingzhi Li, Hefeng Cheng, Xiaoling Huang, Songheng Jin
Summary: This study analyzed the organelle genome information of R. x pulchrum and its related species, revealing the characteristics of their mitochondrial and chloroplast genomes, as well as potential molecular markers. It also discovered gene rearrangement between R. x pulchrum and other species. The study showed that codon usage bias is influenced by mutation and selection, and identified homologous fragments between the chloroplast and mitochondrial genomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Michael Biggel, Magdalena Nuesch-Inderbinen, Christoph Jans, Marc J. A. Stevens, Roger Stephan
Summary: Linezolid is an important last resort antibiotic for treating multidrug-resistant enterococci. This study characterized the genetic context of optrA and poxtA in florfenicol-resistant enterococci isolated from flowing surface water, revealing that they were embedded in transposition units integrated into plasmids or into the chromosomal radC. Additionally, a chromosomally integrated optrA in an Enterococcus raffinosus isolate was described for the first time.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Microbiology
Joseph Wambui, Nicole Cernela, Marc J. A. Stevens, Roger Stephan
Summary: This study identified and characterized isolates within the Clostridium estertheticum complex (CEC) through whole genome sequencing, revealing potential overlaps between different species when using different threshold values for species classification.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Joseph Wambui, Marc J. A. Stevens, Simon Sieber, Nicole Cernela, Vincent Perreten, Roger Stephan
Summary: In this study, the bacteriocin biosynthetic potential of the psychrophilic Clostridium estertheticum complex (CEC) was explored through genome mining and phenotypic screening. Twenty novel bacteriocin biosynthetic gene clusters (BBGC) were discovered, some of which showed antimicrobial activity against closely related clostridia species and clinically relevant pathogens.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Joseph Wambui, Marc J. A. Stevens, Nicole Cernela, Roger Stephan
Summary: The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC) has been linked to the acetone-butyrate-ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. This study compares 50 CEC genomes from 11 CEC species to determine the genetic diversity and factors driving it. The analysis reveals that recombination and gene gain/loss events are important sources of natural variation within CEC, and the presence/absence of the hyp gene cluster is associated with variable gas production in meat.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Julia Isenring, Marc J. A. Stevens, Christoph Jans, Christophe Lacroix, Annelies Geirnaert
Summary: This study investigates the colonization process of Lactiplantibacillus plantarum in the in vitro colonic community, showing that colonization levels are dependent on the microbiota features rather than the introduction parameters. The study also demonstrates that the carrying capacity decreases over time and is correlated with richness and evenness. The findings provide important insights into colonizer-microbiota interactions and probiotic strategies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Christoph Jans, Joseph Wambui, Marc J. A. Stevens, Taurai Tasara
Summary: Staphylococcus aureus infection has a significant impact on the health of both humans and animals in sub-Saharan Africa. The presence of S. aureus in dairy products is prevalent, but little is known about its population structure and genetic characteristics. This research revealed a high diversity of S. aureus strains in dairy products, indicating that milk serves as a reservoir for both human and animal strains. Additionally, a novel putative siderophore was discovered, suggesting possible horizontal gene transfer. These findings emphasize the importance of an integrative One Health approach in addressing S. aureus infections in animals and humans in sub-Saharan Africa.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Veterinary Sciences
Violaine Albane Colon, Kittitat Lugsomya, Hoi Kiu Lam, Lloyd Christian Wahl, Rebecca Sarah Victoria Parkes, Catherine Anne Cormack, Jule Anna Horlbog, Marc Stevens, Roger Stephan, Ioannis Magouras
Summary: This study investigated the prevalence and serotype diversity of Salmonella in turtles sold in wet markets in Hong Kong. It found a high prevalence of Salmonella in the turtles, with considerable serotype diversity. The study also observed resistance to certain antibiotics, including some that are commonly used to treat salmonellosis. Additionally, a multidrug-resistance gene cfr was identified for the first time in Salmonella.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Francis Muchaamba, Ueli von Ah, Roger Stephan, Marc J. A. Stevens, Taurai Tasara
Summary: This study reveals that cold-shock domain family proteins (Csps) play significant roles in nutrient utilization and stress responses in Listeria monocytogenes (Lm), contributing to the public health and food safety impacts of this pathogen.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Magdalena Nueesch-Inderbinen, Andrea Treier, Marc J. A. Stevens, Roger Stephan
Summary: The study assessed the presence of pathogenic bacteria, specifically Shiga toxin-producing Escherichia coli (STEC), in game meat samples from different European countries. PCR analysis detected Shiga-toxin encoding genes in 84% of the samples, with 25% of the same samples containing isolated STEC strains. Various serotypes and sequence types were identified, with some strains carrying virulence factors associated with both STEC and extra-intestinal pathogenic E. coli (ExPEC). The findings suggest that game meat may serve as a potential source of STEC infections in humans, highlighting the importance of safe handling and preparation of such meat to prevent foodborne illnesses.
SCIENTIFIC REPORTS
(2023)
Article
Food Science & Technology
Sara Boss, Roger Stephan, Jule Anna Horlbog, Ioannis Magouras, Violaine Albane Colon, Kittitat Lugsomya, Marc J. A. Stevens, Magdalena Nueesch-Inderbinen
Summary: This study found that about 65% of live edible Chinese frogs collected from wet markets in Hong Kong were carriers of Salmonella, including multiple serotypes. The study also identified a number of antimicrobial resistance genes and virulence determinants, as well as 21% of the isolates being multidrug-resistant. Therefore, public health measures should be implemented to mitigate the risk of Salmonella transmission to humans through handling edible frogs.
Article
Food Science & Technology
Marc J. A. Stevens, Nicole Cernela, Roger Stephan, Angelika Lehner
Summary: Sequencing of Cronobacter sakazakii strains from a powdered infant formula plant over a 15-year period revealed two major sequence types, ST83 and ST4. Genomic comparisons showed clonality of most ST83 and some ST4 strains, with population-specific genes potentially involved in persistence, such as aggregation and stress-resistance genes in ST83 strains and fimbrial genes in ST4 strains. Several antimicrobial resistance genes, including a colistin resistance gene acquired via horizontal gene transfer, were found in these strains. The findings suggest that evolving C. sakazakii populations in an industrial environment may have an impact on public health.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Microbiology
Danai Etter, Ramona Buchel, Tabea Patt, Michael Biggel, Taurai Tasara, Nicole Cernela, Marc J. A. Stevens, Sophia Johler
Summary: The study found that nitrite stress increases staphylococcal enterotoxin C transcription by affecting sec mRNA transcription, but has less pronounced effects on SEC protein expression. Different regulatory knockout mutants showed different responses under stress, indicating that SEC expression is regulated by multiple factors.
FEMS MICROBIOLOGY LETTERS
(2022)
Article
Microbiology
Francis Muchaamba, Athmanya K. Eshwar, Marc J. A. Stevens, Roger Stephan, Taurai Tasara
Summary: Listeria monocytogenes, a bacterium posing challenges to public health and food safety, exhibits variations in virulence and stress resilience among different strains. Strains with different serotypes and genotypes have distinct pathogenicity and survival abilities, which contribute to food product contamination and outbreaks of listeriosis. Genetic and phenotypic differences between strains may play a crucial role in determining virulence and stress sensitivity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Sophie Peterhans, Marc J. A. Stevens, Nicole Cernela, Xaver Sidler, Roger Stephan, Simone Scherrer
Summary: In this study, we report the draft genome sequences of two Actinobacillus pleuropneumoniae serotype 19 strains isolated from two different pig farms in Switzerland in 2018 and 2021, both with a serogroup 3/6/8/12/15 O-antigen locus.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Veterinary Sciences
Jessica Schlicher, Sarah Schmitt, Marc J. A. Stevens, Roger Stephan, Giovanni Ghielmetti
Summary: This study provides further insights into the genetic diversity of Corynebacterium pseudotuberculosis isolates in Switzerland and Liechtenstein, demonstrating the presence of multiple MLSA sequence types over a 15-year period. No specific MLSA sequence types unique to sheep and goats were found.
VETERINARY SCIENCES
(2021)