740 results found
    1. Ecology
    2. Genetics and Genomics

    Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

    Simon Roux et al.
    From public microbial genomes, VirSorter revealed 12,498 viral genome sequences that expand the map of the global virosphere and whose analyses improve understanding of viral taxonomy, evolution and virus-host interactions.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

    Francesco Beghini et al.
    The bioBakery 3 platform enables improved, integrated, and strain-level analysis of microbial communities from large-scale meta-omic data.
    1. Ecology
    2. Microbiology and Infectious Disease

    Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

    Simon Roux et al.
    Single-cell amplified genome sequencing uncovers virus-host interactions in uncultivated sulfur-oxidizing bacteria with relevance to coupled biogeochemical cycling in marine oxygen minimum zones.
    1. Genetics and Genomics

    Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade

    Tom O Delmont et al.
    An in-depth metagenomic analysis of possibly the most abundant and widespread microbial lineage in the surface ocean teases apart evolutionary processes that maintain its genomic heterogeneity and biogeography.
    1. Ecology

    Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

    Jordan G Okie et al.
    Trait-based metagenomic analysis of an ecosystem fertilization experiment shows that genomic traits that affect the costs and rates of biochemical information-processing mediate community assembly.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Genome streamlining in a minute herbivore that manipulates its host plant

    Robert Greenhalgh et al.
    The genome of a tiny tomato pest reveals mechanisms that underlie metazoan genome reduction.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

    Stephan Kamrad et al.
    An open-source python package for phenotype analyses provides a versatile, modular and user-friendly solution to determine complementary fitness-related traits from large-scale assays of microbial colonies.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

    Daniel R Knight et al.
    The Clostridioides difficile taxonomy is characterised by major taxonomic incoherence and clear species boundaries.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

    Kirsten I Bos et al.
    The analysis of 18th century Y. pestis genomes reveals a bacterial lineage that might be responsible for the 400-year period of European plague epidemics from the Renaissance through early modern times.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation

    Elizabeth R Hughes et al.
    Bioinformatics analyses and experiments in mouse models reveal how Escherichia coli accesses the molecular hydrogen pool to boost colonization during acute colitis.

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