Evidence map›Paper›PMID 42907460›Full record

ArticleNature communications2026

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

Lora Khatib, Renee Oles, Alejandra Ríos Hernández, Tyler Myers, Jianshu Zhao, Megha Kumar, Ana Laroya, Veronica Tolosa-Enguis, Nobuko Matsunami, Daisuke Suzuki and 35 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

45 authors.

Lora KhatibDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-6998-8278
Renee OlesDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Alejandra Ríos HernándezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Tyler MyersCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Jianshu ZhaoDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Megha KumarDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Ana LaroyaMicrobiome Innovation in Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
Veronica Tolosa-EnguisMicrobiome Innovation in Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
Nobuko MatsunamiSchool of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.
Daisuke SuzukiSchool of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.ORCID 0000-0003-1750-8516
Nodoka ChibaSchool of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.ORCID 0009-0002-2473-663X
Katharine E GilbertCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Promi DasCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-6733-2059
Jon G SandersCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Lucas PatelDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-8607-2782
Nicole LitwinCrohn's & Colitis Foundation, New York, NY, USA.
Brent NowinskiCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Amanda BirminghamDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-4117-3317
Sawyer FarmerDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0006-4160-9535
Caitriona BrennanDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
MacKenzie BryantDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Caitlin TribelhornDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0002-8788-471X
Karenina Sanders-BodaiDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Charles CowartCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0002-6741-8914
Oliver NizetDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID 0009-0008-8956-3809
Edgar A DiazDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Patrick VeigaUniversité Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France.ORCID 0000-0001-6318-8547
Sudarshan A ShettyDanone Research & Innovation, Utrecht, the Netherlands.ORCID 0000-0001-7280-9915
Jan KnolDanone Research & Innovation, Utrecht, the Netherlands.ORCID 0000-0002-2103-5961
Christophe LayPrecision Nutrition D-Lab, Danone Global Research & Innovation Center, Singapore, Singapore.
Hana KoutnikovaDanone Research & Innovation, Gif sur Yvette, France.ORCID 0000-0001-7763-8983
Soline ChaumontDanone Research & Innovation, Gif sur Yvette, France.ORCID 0000-0002-4084-6057
Julien TapUniversité Paris-Saclay, INRAE, AgroParisTech, UMR1319 MICALIS Institute, Jouy-en-Josas, France.ORCID 0000-0001-8998-5413
Aurélie CotillardDanone Research & Innovation, Gif sur Yvette, France.
Muriel DerrienVIB-KU Leuven Center for Microbiology, Leuven, Belgium.ORCID 0000-0001-8841-9153
Manolo LaiolaDanone Research & Innovation, Gif sur Yvette, France.
Antonio GonzálezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Armando R TovarDepartment of Nutritional Physiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico.
Nimbe TorresDepartment of Nutritional Physiology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico.ORCID 0000-0002-1741-0984
Yolanda SanzMicrobiome Innovation in Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain.ORCID 0000-0002-1615-1976
Takuji YamadaSchool of Life Science and Technology, Institute of Science Tokyo, Tokyo, Japan.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Se Jin SongCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0750-5709
Andrew BartkoDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA. abartko@ucsd.edu.ORCID 0000-0002-1237-2747
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Funding

UC San Diego Medical Scientist Training ProgramT32GM154642 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Neil C Chi, Mary Kathleen Lewinski · 2025 to 2026
$2.9M
NIGMS NIH HHS T32 GM154642
6 · The paper itself

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.

Indexed as

DietGastrointestinal MicrobiomeBacteriaFemaleGenetic VariationGeographyHumansJapanMaleMetagenomeMetagenomicsMexicoSpainUnited KingdomUnited States

Identifiers

PMID42907460
PMCPMC13687547

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.