Skip to main content
Dryad

An evolution-based framework for describing human gut bacteria

Data files

Dec 25, 2023 version files 1.07 GB

Abstract

The human gut microbiome contains many bacterial strains of the same species (‘strain-level variants’). Describing strains in a biologically meaningful manner rather than purely taxonomic objects is an important goal but challenging due to the complexity of strain-level variation. Here, we measured patterns of co-evolution across >7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary history.