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. 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, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution. [Display omitted] • In-depth analyses of 408 Bacteroidales isolated from the gut of healthy humans • Pan-order genomic analyses reveal distinct features of families, genera, and species • Metabolomic diversity of Bacteroidales correlates with their genomic diversity • Documentation of extensive DNA transfer and strain evolution in the human gut Bacteroidales are the most abundant and stable order of bacteria in the healthy human gut microbiota. Comprehensive, in-depth analysis of a large human gut Bacteroidales culture collection by Zhang et al. reveals extensive strain-level genomic and metabolomic diversity and extensive inter-species DNA transfer and strain evolution in the human gut. [ABSTRACT FROM AUTHOR]