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bioRxiv · 10.1101/2023.12.04.569969

An evolution-based framework for describing human gut bacteria

Doran, B. A.·Chen, R. Y.·Giba, H.·Behera, V.·Barat, B.·Sundararajan, A.·Lin, H.·Sidebottom, A.·Pamer, E. G.·Raman, A.
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Abstract

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. One Sentence SummaryDescribing bacterial strains in the human gut by a statistical model that captures their evolutionary history provides insight into their biology.

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Doran, B. A., Chen, R. Y., Giba, H., Behera, V., Barat, B., Sundararajan, A., Lin, H., Sidebottom, A., Pamer, E. G., Raman, A.. 2023-12-05. An evolution-based framework for describing human gut bacteria. https://doi.org/10.1101/2023.12.04.569969

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