A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population
ABSTRACT Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number o...
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American Society for Microbiology
2025-07-01
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00544-25 |
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| author | Lora Khatib Se Jin Song Amanda H. Dilmore Jon G. Sanders Caitriona Brennan Alejandra Rios Hernandez Tyler Myers Renee Oles Sawyer Farmer Charles Cowart Amanda Birmingham Edgar A. Diaz Oliver Nizet Kat Gilbert Nicole Litwin Promi Das Brent Nowinski Mackenzie Bryant Caitlin Tribelhorn Karenina Sanders-Bodai Soline Chaumont Jan Knol Guus Roeselers Manolo Laiola Sudarshan A. Shetty Patrick Veiga Julien Tap Muriel Derrien Hana Koutnikova Aurélie Cotillard Christophe Lay Armando R. Tovar Nimbe Torres Liliana Arteaga Antonio González Daniel McDonald Andrew Bartko Rob Knight |
| author_facet | Lora Khatib Se Jin Song Amanda H. Dilmore Jon G. Sanders Caitriona Brennan Alejandra Rios Hernandez Tyler Myers Renee Oles Sawyer Farmer Charles Cowart Amanda Birmingham Edgar A. Diaz Oliver Nizet Kat Gilbert Nicole Litwin Promi Das Brent Nowinski Mackenzie Bryant Caitlin Tribelhorn Karenina Sanders-Bodai Soline Chaumont Jan Knol Guus Roeselers Manolo Laiola Sudarshan A. Shetty Patrick Veiga Julien Tap Muriel Derrien Hana Koutnikova Aurélie Cotillard Christophe Lay Armando R. Tovar Nimbe Torres Liliana Arteaga Antonio González Daniel McDonald Andrew Bartko Rob Knight |
| author_sort | Lora Khatib |
| collection | DOAJ |
| description | ABSTRACT Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.IMPORTANCEAn analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health. |
| format | Article |
| id | doaj-art-ffc01150b7704b59bb70f6a525a81ef3 |
| institution | DOAJ |
| issn | 2379-5077 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj-art-ffc01150b7704b59bb70f6a525a81ef32025-08-20T03:08:21ZengAmerican Society for MicrobiologymSystems2379-50772025-07-0110710.1128/msystems.00544-25A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and populationLora Khatib0Se Jin Song1Amanda H. Dilmore2Jon G. Sanders3Caitriona Brennan4Alejandra Rios Hernandez5Tyler Myers6Renee Oles7Sawyer Farmer8Charles Cowart9Amanda Birmingham10Edgar A. Diaz11Oliver Nizet12Kat Gilbert13Nicole Litwin14Promi Das15Brent Nowinski16Mackenzie Bryant17Caitlin Tribelhorn18Karenina Sanders-Bodai19Soline Chaumont20Jan Knol21Guus Roeselers22Manolo Laiola23Sudarshan A. Shetty24Patrick Veiga25Julien Tap26Muriel Derrien27Hana Koutnikova28Aurélie Cotillard29Christophe Lay30Armando R. Tovar31Nimbe Torres32Liliana Arteaga33Antonio González34Daniel McDonald35Andrew Bartko36Rob Knight37Department of Pediatrics, University of California San Diego, La Jolla, California, USACenter for Microbiome Innovation, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USACenter for Microbiome Innovation, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USACenter for Microbiome Innovation, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USACrohn’s and Colitis Foundation, New York, New York, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USACenter for Microbiome Innovation, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADanone Research and Innovation, Gif sur Yvette, FranceDanone Research and Innovation, Utrecht, the NetherlandsDanone Research and Innovation, Utrecht, the NetherlandsDanone Research and Innovation, Utrecht, the NetherlandsDanone Research and Innovation, Utrecht, the NetherlandsDanone Research and Innovation, Gif sur Yvette, FranceDanone Research and Innovation, Gif sur Yvette, FranceDanone Research and Innovation, Gif sur Yvette, FranceDanone Research and Innovation, Gif sur Yvette, FranceDanone Research and Innovation, Gif sur Yvette, FrancePrecision Nutrition D-Lab, Danone Global Research and Innovation Center, Singapore, SingaporeInstituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, MéxicoInstituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, MéxicoInstituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, MéxicoDepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USADepartment of Pediatrics, University of California San Diego, La Jolla, California, USAABSTRACT Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.IMPORTANCEAn analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.https://journals.asm.org/doi/10.1128/msystems.00544-25human microbiomemetagenomicsdietPrevotellaFaecalibacterium |
| spellingShingle | Lora Khatib Se Jin Song Amanda H. Dilmore Jon G. Sanders Caitriona Brennan Alejandra Rios Hernandez Tyler Myers Renee Oles Sawyer Farmer Charles Cowart Amanda Birmingham Edgar A. Diaz Oliver Nizet Kat Gilbert Nicole Litwin Promi Das Brent Nowinski Mackenzie Bryant Caitlin Tribelhorn Karenina Sanders-Bodai Soline Chaumont Jan Knol Guus Roeselers Manolo Laiola Sudarshan A. Shetty Patrick Veiga Julien Tap Muriel Derrien Hana Koutnikova Aurélie Cotillard Christophe Lay Armando R. Tovar Nimbe Torres Liliana Arteaga Antonio González Daniel McDonald Andrew Bartko Rob Knight A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population mSystems human microbiome metagenomics diet Prevotella Faecalibacterium |
| title | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| title_full | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| title_fullStr | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| title_full_unstemmed | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| title_short | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| title_sort | three country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
| topic | human microbiome metagenomics diet Prevotella Faecalibacterium |
| url | https://journals.asm.org/doi/10.1128/msystems.00544-25 |
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