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    1. Ecology

    Multistability and regime shifts in microbial communities explained by competition for essential nutrients

    Veronika Dubinkina et al.
    Multistability and regime shifts are common and species diversity is high in microbial communities when nutrient supplies are balanced and competing species have different stoichiometries of essential nutrients.
    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.
    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. Ecology

    The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis

    Valeria Souza et al.
    At Cuatro Ciénegas, the ancestral niche conditions of the ancient shores of Laurentia persisted along with its microbial communities that have been coevolving for a very long time.
    1. Ecology
    2. Evolutionary Biology

    Effects of domestication on the gut microbiota parallel those of human industrialization

    Aspen T Reese et al.
    Gut microbial signatures of domestication parallel those of industrialization, implicating shared ecological drivers.
    1. Microbiology and Infectious Disease

    A novel decoy strategy for polymyxin resistance in Acinetobacter baumannii

    Jaeeun Park et al.
    Outer membrane vesicles serve as decoys to reduce the chance of direct polymyxin B (PMB) binding to cells, which partly explains why many clinical isolates and microbial communities can be protected against PMB treatment.
    1. Immunology and Inflammation

    Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity

    Juan L Mendoza et al.
    Potential for specific microbiome-directed, MHC-restricted shaping of a commonly selected HIV-specific CD8+ T cell population was suggested by MHC class I yeast display-based peptide screening approaches.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

    Evan T Saitta et al.
    Subterranean fossil bone hosts a living microbiome different from the surrounding sediment without evidence of original protein preservation.
    1. Plant Biology

    Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field

    Arne Weinhold et al.
    The attempt to manipulate a microbiome in planta to study the ecological consequences under field conditions leaves plants and their microbes surprisingly unimpressed.
    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.