{
  "abstract": "Human diet and lifestyle vary widely across cultures, shaping global diversity in gut microbiome composition and function. However, comparable cross-population studies have been limited by methodological heterogeneity. The Human Diets and Microbiome Initiative (THDMI) integrates standardized recruitment, dietary assessment, and shotgun metagenomics across 1,976 participants from the United States, United Kingdom, Spain, Mexico, and Japan to disentangle biological from technical variation. We observed pronounced geographic differences in nutrient intake, food consumption, and microbial composition, with both shared and country-specific features linked to diet. Sparse canonical correlation and machine-learning analyses revealed that microbiome-diet associations were largely population-specific, with limited cross-country generalization. Strain-level analyses further uncovered significant genomic differentiation of gut microbes, consistent with localized dietary and ecological differences. Together, these results show that while core microbial responses to healthy eating exist, the structure and function of the human gut microbiome varies strongly with culture, geography, and long-term dietary practices.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.",
    "Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA.",
    "Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.",
    "Department of Mathematics, University of California San Diego, La Jolla, CA, USA.",
    "Department of Cognitive Science, University of California San Diego, La Jolla, CA, USA.",
    "Microbiome Innovation in Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain.",
    "School of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.",
    "Gutz Analytics, Boulder, CO, USA.",
    "Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.",
    "Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA.",
    "Crohn's & Colitis Foundation, New York, NY, USA.",
    "Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.",
    "Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.",
    "Department of Research & Health Promotion, San Ysidro Health, San Diego, CA, USA.",
    "Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France.",
    "Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 MICALIS Institute, Jouy-en-Josas, France.",
    "Danone Research & Innovation, Utrecht, the Netherlands.",
    "Precision Nutrition D-Lab, Danone Global Research & Innovation Center, Singapore, Singapore.",
    "Danone Research & Innovation, Gif sur Yvette, France.",
    "VIB-KU Leuven Center for Microbiology, Leuven, Belgium.",
    "Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.",
    "Department of Nutritional Physiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico.",
    "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. abartko@ucsd.edu.",
    "Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. abartko@ucsd.edu.",
    "Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. abartko@ucsd.edu.",
    "Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.",
    "Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.",
    "Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.",
    "Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study, Hong Kong, China."
  ],
  "article_type": "research support, non u.s. gov't",
  "arxiv": null,
  "author_total": 45,
  "authors": [
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        1
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      "name": "Lora Khatib",
      "orcid": "0000-0002-6998-8278"
    },
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      ],
      "name": "Renee Oles"
    },
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      "name": "Alejandra Ríos Hernández"
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        2
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      "name": "Tyler Myers"
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        0
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        0,
        3,
        4
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      "name": "Megha Kumar"
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      "name": "Ana Laroya"
    },
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        5
      ],
      "name": "Veronica Tolosa-Enguis"
    },
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      "affs": [
        6
      ],
      "name": "Nobuko Matsunami"
    },
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        6
      ],
      "name": "Daisuke Suzuki",
      "orcid": "0000-0003-1750-8516"
    },
    {
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        6
      ],
      "name": "Nodoka Chiba",
      "orcid": "0009-0002-2473-663X"
    },
    {
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        2
      ],
      "name": "Katharine E Gilbert"
    },
    {
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      "name": "Promi Das",
      "orcid": "0000-0001-6733-2059"
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      "name": "Jon G Sanders"
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      "name": "Lucas Patel",
      "orcid": "0000-0001-8607-2782"
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      "name": "Nicole Litwin"
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      "name": "Brent Nowinski"
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        0
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      "name": "Amanda Birmingham",
      "orcid": "0000-0002-4117-3317"
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        0
      ],
      "name": "Sawyer Farmer",
      "orcid": "0009-0006-4160-9535"
    },
    {
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        0,
        11
      ],
      "name": "Caitriona Brennan"
    },
    {
      "affs": [
        0
      ],
      "name": "MacKenzie Bryant"
    },
    {
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        0
      ],
      "name": "Caitlin Tribelhorn",
      "orcid": "0009-0002-8788-471X"
    },
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        0
      ],
      "name": "Karenina Sanders-Bodai"
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      "name": "Charles Cowart",
      "orcid": "0009-0002-6741-8914"
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        12
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      "name": "Oliver Nizet",
      "orcid": "0009-0008-8956-3809"
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      ],
      "name": "Edgar A Diaz",
      "orcid": "0000-0002-9076-6549"
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      "name": "Patrick Veiga",
      "orcid": "0000-0001-6318-8547"
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      ],
      "name": "Sudarshan A Shetty",
      "orcid": "0000-0001-7280-9915"
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      ],
      "name": "Jan Knol",
      "orcid": "0000-0002-2103-5961"
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    {
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        17
      ],
      "name": "Christophe Lay"
    },
    {
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        18
      ],
      "name": "Hana Koutnikova",
      "orcid": "0000-0001-7763-8983"
    },
    {
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        18
      ],
      "name": "Soline Chaumont",
      "orcid": "0000-0002-4084-6057"
    },
    {
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        15
      ],
      "name": "Julien Tap",
      "orcid": "0000-0001-8998-5413"
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        18
      ],
      "name": "Aurélie Cotillard"
    },
    {
      "affs": [
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        20
      ],
      "name": "Muriel Derrien",
      "orcid": "0000-0001-8841-9153"
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    {
      "affs": [
        18
      ],
      "name": "Manolo Laiola"
    },
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      "name": "Antonio González"
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      "name": "Armando R Tovar"
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      "name": "Nimbe Torres",
      "orcid": "0000-0002-1741-0984"
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        5
      ],
      "name": "Yolanda Sanz",
      "orcid": "0000-0002-1615-1976"
    },
    {
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        6
      ],
      "name": "Takuji Yamada"
    },
    {
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        0
      ],
      "name": "Daniel McDonald"
    },
    {
      "affs": [
        2
      ],
      "name": "Se Jin Song",
      "orcid": "0000-0003-0750-5709"
    },
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      "affs": [
        22,
        23,
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      ],
      "name": "Andrew Bartko",
      "orcid": "0000-0002-1237-2747"
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      "name": "Rob Knight"
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  ],
  "bibtex": "https://research.draconitic.com/paper/0ha4eq209ad45.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-77928-9",
  "fulltext_url": "https://europepmc.org/articles/PMC13687547",
  "id": "0ha4eq209ad45",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://europepmc.org/article/MED/42907460",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7213876306",
  "pdf_url": "https://europepmc.org/articles/PMC13687547?pdf=render",
  "pmcid": "PMC13687547",
  "pmid": "42907460",
  "published": "2026-09-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0ha4eq209ad45.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:57Z",
      "native_id": "MED:42907460",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42907460"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.",
  "title_text": "Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:57Z",
  "url": "https://research.draconitic.com/paper/0ha4eq209ad45",
  "venue": "Nature communications",
  "versions": []
}