An evolution-based framework for describing human gut bacteria.

Autor: Doran BA; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637.; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637., Chen RY; Department of Psychiatry, University of Washington, Seattle, WA, 98195., Giba H; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637.; Department of Pathology, University of Chicago, Chicago, IL, 60637., Behera V; Department of Medicine, University of Chicago, Chicago, IL, 60637., Barat B; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637., Sundararajan A; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637., Lin H; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637., Sidebottom A; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637., Pamer EG; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637.; Department of Medicine, University of Chicago, Chicago, IL, 60637., Raman AS; Duchossois Family Institute, University of Chicago, Chicago, IL, 60637.; Department of Pathology, University of Chicago, Chicago, IL, 60637.; Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637.
Jazyk: angličtina
Zdroj: BioRxiv : the preprint server for biology [bioRxiv] 2023 Dec 05. Date of Electronic Publication: 2023 Dec 05.
DOI: 10.1101/2023.12.04.569969
Abstrakt: 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.
Databáze: MEDLINE
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