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phylogeny

  • Open Access
    An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among <span class="named-content genus-species" id="named-content-1">Listeria monocytogenes</span> Isolates in Outdoor Environments and Poultry Processing Plants
    Food Microbiology | Spotlight
    An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants

    We have developed an open-source tool (https://github.com/swarnalilouha/Haplo-ST) that provides allele-based subtyping of L. monocytogenes isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree...

    Swarnali Louha, Richard J. Meinersmann, Zaid Abdo, Mark E. Berrang, Travis C. Glenn
  • Whole-Genome Comparisons of <em>Staphylococcus agnetis</em> Isolates from Cattle and Chickens
    Evolutionary and Genomic Microbiology
    Whole-Genome Comparisons of Staphylococcus agnetis Isolates from Cattle and Chickens

    Staphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat-type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with...

    Abdulkarim Shwani, Pamela R. F. Adkins, Nnamdi S. Ekesi, Adnan Alrubaye, Michael J. Calcutt, John R. Middleton, Douglas D. Rhoads
  • Open Access
    Potential Enterotoxicity of Phylogenetically Diverse <span class="named-content genus-species" id="named-content-1">Bacillus cereus Sensu Lato</span> Soil Isolates from Different Geographical Locations
    Evolutionary and Genomic Microbiology
    Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations

    This research offers a new route for a wider understanding of the dependency between pathogenicity and phylogeny of a natural bacterial population, specifically within Bacillus cereus sensu lato, that is widely distributed around the world and easily transferred into food products. Our study indicates differences in the phylogenetic and geographical distributions of...

    Justyna Malgorzata Drewnowska, Natalia Stefanska, Magdalena Czerniecka, Grzegorz Zambrowski, Izabela Swiecicka
  • Diguanylate Cyclases and Phosphodiesterases Required for Basal-Level c-di-GMP in <em>Pseudomonas aeruginosa</em> as Revealed by Systematic Phylogenetic and Transcriptomic Analyses
    Genetics and Molecular Biology
    Diguanylate Cyclases and Phosphodiesterases Required for Basal-Level c-di-GMP in Pseudomonas aeruginosa as Revealed by Systematic Phylogenetic and Transcriptomic Analyses

    Pseudomonas aeruginosa is an opportunistic pathogen that can cause infections in animals, humans, and plants. The formation of biofilms by P. aeruginosa is the central mode of action to persist in hosts and evade immune and antibiotic attacks. Cyclic-di-GMP (c-di-GMP) is an important second...

    Qing Wei, Sebastien Leclercq, Pramod Bhasme, Anming Xu, Bin Zhu, Yuhuan Zhang, Miaokun Zhang, Shiwei Wang, Luyan Z. Ma
  • Open Access
    Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase <em>In Vitro</em>
    Enzymology and Protein Engineering | Spotlight
    Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase In Vitro

    Establishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase from Kitasatospora aureofaciens is of particular interest for several reasons. First, the phylogenetic analysis of...

    Peter L. Herzog, Leander Sützl, Beate Eisenhut, Daniel Maresch, Dietmar Haltrich, Christian Obinger, Clemens K. Peterbauer
  • Open Access
    Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant <em>Enterococcus faecalis</em> in New Zealand
    Public and Environmental Health Microbiology | Spotlight
    Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand

    Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence.

    Rowena Rushton-Green, Rachel L. Darnell, George Taiaroa, Glen P. Carter, Gregory M. Cook, Xochitl C. Morgan
  • Open Access
    Insights into the Phylogeny, Nodule Function, and Biogeographic Distribution of Microsymbionts Nodulating the Orphan Kersting’s Groundnut [<em>Macrotyloma geocarpum</em> (Harms) Marechal &amp; Baudet] in African Soils
    Plant Microbiology
    Insights into the Phylogeny, Nodule Function, and Biogeographic Distribution of Microsymbionts Nodulating the Orphan Kersting’s Groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] in African Soils

    Rhizobia play important roles in agroecosystems, where they contribute to improving overall soil health through their symbiotic relationship with legumes. This study explored the microsymbionts nodulating Kersting’s groundnut, a neglected orphan legume. The results revealed the presence of different bradyrhizobial populations with high N2-fixing efficiencies as the dominant symbionts of this legume across diverse...

    Mustapha Mohammed, Sanjay K. Jaiswal, Felix D. Dakora
  • Dissecting the Evolutionary Development of the Species <em>Bifidobacterium animalis</em> through Comparative Genomics Analyses
    Microbial Ecology
    Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses

    The majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the gastrointestinal tracts of different animals, including mammals and birds. The present study allowed us to reconstruct the pangenome of this taxon, including the genome contents...

    Gabriele Andrea Lugli, Walter Mancino, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Stefania Napoli, Marta Mangifesta, Alice Viappiani, Rosaria Anzalone, Giulia Longhi, Douwe van Sinderen, Marco Ventura, Francesca Turroni
  • Host Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical Enteropathogenic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Strains
    Public and Environmental Health Microbiology
    Host Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical Enteropathogenic Escherichia coli Strains

    Atypical enteropathogenic Escherichia coli (aEPEC) is a diarrheagenic type of E. coli, as it possesses the intimin gene (eae) for attachment and effacement on epithelium. Since aEPEC is ubiquitous even in developed countries, we previously used molecular epidemiological methods to...

    Md Shafiullah Parvej, Hiromi Nakamura, Md Ashraful Alam, Lili Wang, Shaobo Zhang, Kazuo Emura, Eriko Kage-Nakadai, Takayuki Wada, Yukiko Hara-Kudo, Yoshikazu Nishikawa
  • Food Microbiology
    Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification
    Elisa Salvetti, Hugh M. B. Harris, Giovanna E. Felis, Paul W. O'Toole

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