Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution. ### Competing Interest Statement E.G.P. serves on the advisory board of Diversigen; is an inventor on patent applications WPO2015179437A1, titled 'Methods and compositions for reducing Clostridium difficile infection', and WO2017091753A1, titled 'Methods and compositions for reducing vancomycin-resistant enterococci infection or colonization'; and receives royalties from Seres Therapeutics, Inc. The other authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this manuscript.