Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation

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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Publication Details

Journal
Nature Communications
Published
2026-09-21
DOI
https://doi.org/10.1038/s41467-026-77928-9
Primary Topic
Gut microbiota and health
Type
article
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article

Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation

Katharine Gilbert, Daniel McDonald, Se Jin Song, Nimbe Torres et al.
Nature Communications
Gut microbiota and health
article

Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation

Katharine Gilbert, Daniel McDonald, Se Jin Song, Nimbe Torres, Charles Cowart, Sudarshan Anand Shetty, Lora A. Khatib, Patrick Veiga, Caitlin Tribelhorn, Muriel Derrien, Andrew P. Bartko, Rob Knight, Daisuke Suzuki, Takuji Yamada, Soline Chaumont, Sawyer H. Farmer, Promi Das, Nodoka Chiba, Lucas Patel, Aurélie Cotillard, Yolanda Sanz, Amanda Birmingham, Hana Koutníková, Oliver Nizet, Caitriona Brennan, Jan Knol, Manolo Laiola, Brent Nowinski, Julien Tap, Edgar A. Diaz, Megha Kumar, Karenina Sanders-Bodai, Alejandra Ríos Hernández, Tyler Myers, Renee Oles, Nobuko Matsunami, Jon G. Sanders, Armando R. Tovar, Christophe Lay, MacKenzie Bryant, Antonio González, Nicole Litwin, Ana Laroya, Veronica Tolosa-Enguis, Jianshu Zhao
article en

Abstract

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.

Nature Communications
DSM (Netherlands) (NL), Johns Hopkins University (US), Rega Institute for Medical Research (BE), Université Paris-Saclay (FR), Microbiologie de l’alimentation au service de la santé (FR), University of California San Diego (US), Systems Analytics (United States) (US), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (MX), Danone (Netherlands) (NL), Instituto de Agroquímica y Tecnología de Alimentos (ES), EP Analytics (United States) (US), Life Science Institute (JP), VIB-KU Leuven Center for Microbiology (BE), San Ysidro Health (US), La Jolla Bioengineering Institute (US), National Research Council (LK), Crohn's and Colitis Foundation (US), KU Leuven (BE)
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