Prehistoric global migration of vanishing gut microbes with humans.
20 affiliations
- 1Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- 2Department of Applied Physics, Stanford University, Stanford, CA, USA.
- 3Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
- 4Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA.
- 5Department of Anthropology, University of Washington, Seattle, WA, USA.
- 6Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
- 7School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
- 8Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
- 9Institute of Human Origins, Arizona State University, Tempe, AZ, USA.
- 10Economic Science Institute, Chapman University, Orange, CA, USA.
- 11Toulouse School of Economics, Toulouse, France.
- 12Universidad Mayor de San Simón, Cochabamba, Bolivia.
- 13Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- 14Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- 15Department of Applied Physics, Stanford University, Stanford, CA, USA. [email protected].
- 16Department of Biology, Stanford University, Stanford, CA, USA. [email protected].
- 17Chan Zuckerberg Biohub, San Francisco, CA, USA. [email protected].
- 18Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. [email protected].
- 19Chan Zuckerberg Biohub, San Francisco, CA, USA. [email protected].
- 20Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA. [email protected].
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 populations²⁻⁶. 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.
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BibTeX
@article{carter2026prehistoric,
title = {{Prehistoric global migration of vanishing gut microbes with humans.}},
author = {Matthew M Carter and Zhiru Liu and Matthew R Olm and Melanie Martin and Daniel D Sprockett and Parsa Ghadermazi and Benjamin C Trumble and Hillard Kaplan and Jonathan Stieglitz and Daniel Eid Rodriguez and David A Relman and Erica D Sonnenburg and Michael Gurven and Benjamin H Good and Justin L Sonnenburg},
journal = {Nature},
year = {2026},
month = oct,
doi = {10.1038/s41586-026-11106-1},
url = {https://europepmc.org/article/MED/42844483},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Prehistoric global migration of vanishing gut microbes with humans.
AU - Matthew M Carter
AU - Zhiru Liu
AU - Matthew R Olm
AU - Melanie Martin
AU - Daniel D Sprockett
AU - Parsa Ghadermazi
AU - Benjamin C Trumble
AU - Hillard Kaplan
AU - Jonathan Stieglitz
AU - Daniel Eid Rodriguez
AU - David A Relman
AU - Erica D Sonnenburg
AU - Michael Gurven
AU - Benjamin H Good
AU - Justin L Sonnenburg
PY - 2026
DA - 2026/10/07
JO - Nature
DO - 10.1038/s41586-026-11106-1
UR - https://europepmc.org/article/MED/42844483
AB - 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 populations²⁻⁶. 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.
SN - 0028-0836
SN - 1476-4687
ER -