{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.",
    "Department of Applied Physics, Stanford University, Stanford, CA, USA.",
    "Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.",
    "Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA.",
    "Department of Anthropology, University of Washington, Seattle, WA, USA.",
    "Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.",
    "School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.",
    "Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.",
    "Institute of Human Origins, Arizona State University, Tempe, AZ, USA.",
    "Economic Science Institute, Chapman University, Orange, CA, USA.",
    "Toulouse School of Economics, Toulouse, France.",
    "Universidad Mayor de San Simón, Cochabamba, Bolivia.",
    "Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.",
    "Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.",
    "Department of Applied Physics, Stanford University, Stanford, CA, USA. bhgood@stanford.edu.",
    "Department of Biology, Stanford University, Stanford, CA, USA. bhgood@stanford.edu.",
    "Chan Zuckerberg Biohub, San Francisco, CA, USA. bhgood@stanford.edu.",
    "Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. jsonnenburg@stanford.edu.",
    "Chan Zuckerberg Biohub, San Francisco, CA, USA. jsonnenburg@stanford.edu.",
    "Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA. jsonnenburg@stanford.edu."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Matthew M Carter"
    },
    {
      "affs": [
        1
      ],
      "name": "Zhiru Liu",
      "orcid": "0000-0002-2604-631X"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Matthew R Olm",
      "orcid": "0000-0001-5540-350X"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Melanie Martin"
    },
    {
      "affs": [
        5
      ],
      "name": "Daniel D Sprockett"
    },
    {
      "affs": [
        2
      ],
      "name": "Parsa Ghadermazi"
    },
    {
      "affs": [
        6,
        7,
        8
      ],
      "name": "Benjamin C Trumble",
      "orcid": "0000-0003-3201-0628"
    },
    {
      "affs": [
        9
      ],
      "name": "Hillard Kaplan",
      "orcid": "0000-0002-7398-7358"
    },
    {
      "affs": [
        10
      ],
      "name": "Jonathan Stieglitz",
      "orcid": "0000-0001-5985-9643"
    },
    {
      "affs": [
        11
      ],
      "name": "Daniel Eid Rodriguez"
    },
    {
      "affs": [
        0,
        12,
        13
      ],
      "name": "David A Relman",
      "orcid": "0000-0001-8331-1354"
    },
    {
      "affs": [
        0
      ],
      "name": "Erica D Sonnenburg"
    },
    {
      "affs": [
        3
      ],
      "name": "Michael Gurven"
    },
    {
      "affs": [
        14,
        15,
        16
      ],
      "name": "Benjamin H Good",
      "orcid": "0000-0002-7757-3347"
    },
    {
      "affs": [
        17,
        18,
        19
      ],
      "name": "Justin L Sonnenburg",
      "orcid": "0000-0003-2299-6817"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dstr6qqgpp2m1.bib",
  "cited_by": 1,
  "doi": "10.1038/s41586-026-11106-1",
  "fulltext_url": "https://europepmc.org/articles/PMC13686943",
  "id": "dstr6qqgpp2m1",
  "issns": [
    "0028-0836",
    "1476-4687"
  ],
  "landing_url": "https://europepmc.org/article/MED/42844483",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7220844731",
  "pdf_url": "https://europepmc.org/articles/PMC13686943?pdf=render",
  "pmcid": "PMC13686943",
  "pmid": "42844483",
  "published": "2026-10-07",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/dstr6qqgpp2m1.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "MED:42844483",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42844483"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Prehistoric global migration of vanishing gut microbes with humans.",
  "title_text": "Prehistoric global migration of vanishing gut microbes with humans.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/dstr6qqgpp2m1",
  "venue": "Nature",
  "versions": []
}