An evolution-based framework for describing human gut bacteria

The human gut microbiome contains many bacterial strains of the same species ('strain-level variants'). Describing strains in a biologically meaningful way rather than purely taxonomically is an important goal but challenging due to the genetic complexity of strain-level variation. Here, w...

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Published inbioRxiv : the preprint server for biology
Main Authors Doran, Benjamin A, Chen, Robert Y, Giba, Hannah, Behera, Vivek, Barat, Bidisha, Sundararajan, Anitha, Lin, Huaiying, Sidebottom, Ashley, Pamer, Eric G, Raman, Arjun S
Format Journal Article
LanguageEnglish
Published United States 05.12.2023
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Summary:The human gut microbiome contains many bacterial strains of the same species ('strain-level variants'). Describing strains in a biologically meaningful way rather than purely taxonomically is an important goal but challenging due to the genetic 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.