Peer-reviewedCC BYNature communications
Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.
29 affiliations
- 1Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- 2Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
- 3Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- 4Department of Mathematics, University of California San Diego, La Jolla, CA, USA.
- 5Department of Cognitive Science, University of California San Diego, La Jolla, CA, USA.
- 6Microbiome Innovation in Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
- 7School of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.
- 8Gutz Analytics, Boulder, CO, USA.
- 9Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- 10Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA.
- 11Crohn's & Colitis Foundation, New York, NY, USA.
- 12Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
- 13Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- 14Department of Research & Health Promotion, San Ysidro Health, San Diego, CA, USA.
- 15Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France.
- 16Université Paris-Saclay, INRAE, AgroParisTech, UMR1319 MICALIS Institute, Jouy-en-Josas, France.
- 17Danone Research & Innovation, Utrecht, the Netherlands.
- 18Precision Nutrition D-Lab, Danone Global Research & Innovation Center, Singapore, Singapore.
- 19Danone Research & Innovation, Gif sur Yvette, France.
- 20VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- 21Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
- 22Department of Nutritional Physiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico.
- 23Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. [email protected].
- 24Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. [email protected].
- 25Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. [email protected].
- 26Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- 27Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- 28Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
- 29Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study, Hong Kong, China.
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.
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BibTeX
@article{khatib2026fivecountry,
title = {{Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.}},
author = {Lora Khatib and Renee Oles and Alejandra Ríos Hernández and Tyler Myers and Jianshu Zhao and Megha Kumar and Ana Laroya and Veronica Tolosa-Enguis and Nobuko Matsunami and Daisuke Suzuki and Nodoka Chiba and Katharine E Gilbert and Promi Das and Jon G Sanders and Lucas Patel and Nicole Litwin and Brent Nowinski and Amanda Birmingham and Sawyer Farmer and Caitriona Brennan and MacKenzie Bryant and Caitlin Tribelhorn and Karenina Sanders-Bodai and Charles Cowart and Oliver Nizet and Edgar A Diaz and Patrick Veiga and Sudarshan A Shetty and Jan Knol and Christophe Lay and Hana Koutnikova and Soline Chaumont and Julien Tap and Aurélie Cotillard and Muriel Derrien and Manolo Laiola and Antonio González and Armando R Tovar and Nimbe Torres and Yolanda Sanz and Takuji Yamada and Daniel McDonald and Se Jin Song and Andrew Bartko and Rob Knight},
journal = {Nature communications},
year = {2026},
month = sep,
doi = {10.1038/s41467-026-77928-9},
url = {https://europepmc.org/article/MED/42907460},
note = {CC BY},
}
RIS
TY - JOUR
TI - Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.
AU - Lora Khatib
AU - Renee Oles
AU - Alejandra Ríos Hernández
AU - Tyler Myers
AU - Jianshu Zhao
AU - Megha Kumar
AU - Ana Laroya
AU - Veronica Tolosa-Enguis
AU - Nobuko Matsunami
AU - Daisuke Suzuki
AU - Nodoka Chiba
AU - Katharine E Gilbert
AU - Promi Das
AU - Jon G Sanders
AU - Lucas Patel
AU - Nicole Litwin
AU - Brent Nowinski
AU - Amanda Birmingham
AU - Sawyer Farmer
AU - Caitriona Brennan
AU - MacKenzie Bryant
AU - Caitlin Tribelhorn
AU - Karenina Sanders-Bodai
AU - Charles Cowart
AU - Oliver Nizet
AU - Edgar A Diaz
AU - Patrick Veiga
AU - Sudarshan A Shetty
AU - Jan Knol
AU - Christophe Lay
AU - Hana Koutnikova
AU - Soline Chaumont
AU - Julien Tap
AU - Aurélie Cotillard
AU - Muriel Derrien
AU - Manolo Laiola
AU - Antonio González
AU - Armando R Tovar
AU - Nimbe Torres
AU - Yolanda Sanz
AU - Takuji Yamada
AU - Daniel McDonald
AU - Se Jin Song
AU - Andrew Bartko
AU - Rob Knight
PY - 2026
DA - 2026/09/21
JO - Nature communications
DO - 10.1038/s41467-026-77928-9
UR - https://europepmc.org/article/MED/42907460
AB - 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.
SN - 2041-1723
ER -