Prehistoric global migration of vanishing gut microbes with humans

Matthew M. Carter, Zhiru Liu, Matthew R. Olm, Melanie Martin, Daniel D. Sprockett, Parsa Ghadermazi, Benjamin C. Trumble, Hillard Kaplan, Jonathan Stieglitz, Daniel Eid Rodriguez, David A. Relman, Erica D. Sonnenburg, Michael Gurven, Benjamin H. Good and Justin L. Sonnenburg
Additional contact information
Matthew M. Carter: Unknown
Zhiru Liu: Unknown
Matthew R. Olm: Unknown
Melanie Martin: Unknown
Daniel D. Sprockett: Unknown
Parsa Ghadermazi: Unknown
Benjamin C. Trumble: Unknown
Hillard Kaplan: TSE-R - Toulouse School of Economics - UT Capitole - Université Toulouse Capitole - Comue de Toulouse - Communauté d'universités et établissements de Toulouse - EHESS - École des hautes études en sciences sociales - CNRS - Centre National de la Recherche Scientifique - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, IAST - Institute for Advanced Study in Toulouse
Jonathan Stieglitz: TSE-R - Toulouse School of Economics - UT Capitole - Université Toulouse Capitole - Comue de Toulouse - Communauté d'universités et établissements de Toulouse - EHESS - École des hautes études en sciences sociales - CNRS - Centre National de la Recherche Scientifique - INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, IAST - Institute for Advanced Study in Toulouse
Daniel Eid Rodriguez: Unknown
David A. Relman: Unknown
Erica D. Sonnenburg: Unknown
Michael Gurven: Unknown
Benjamin H. Good: Unknown
Justin L. Sonnenburg: Unknown

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Abstract: The gut microbiome is crucial for health and is affected strongly by lifestyle1. Many microorganisms commonly found in non-industrialized populations are disappearing or have become extinct in industrialized populations2,3,4,5,6. Studying which microorganisms have been long-term residents of the human gut and may have co-evolved with humans2,7,8 could provide insights into how microbial biodiversity loss affects human health. However, the genetic complexities of microbial evolution and the plasticity of gut microbiome composition have made it challenging to resolve the evolutionary history of these long-term associations. Here we performed deep metagenomic sequencing of the Tsimane horticulturalists of Bolivia and compared their gut microbiomes with those of the Hadza hunter-gatherers of Tanzania3. These two populations, whose ancestors have been separated for tens of thousands of years, share 1,231 microbial species, most of which are rare in or absent from industrialized populations. Population genetic analyses of 636 of the shared species revealed patterns of microbial divergence and gene flow consistent with prehistoric human co-migration, with estimated split times that approximately align with human migration out of Africa and into the Americas. Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia. However, many of these species are now vanishing from industrialized populations and the consequences for human health remain uncertain.

Date: 2026-10-07
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Published in Nature, 2026, ⟨10.1038/s41586-026-11106-1⟩

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Persistent link: https://EconPapers.repec.org/RePEc:hal:journl:hal-05788316

DOI: 10.1038/s41586-026-11106-1

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