A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population
An 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 micr...
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| Published in | mSystems Vol. 10; no. 7; p. e0054425 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Society for Microbiology
22.07.2025
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| Subjects | |
| Online Access | Get full text |
| ISSN | 2379-5077 2379-5077 |
| DOI | 10.1128/msystems.00544-25 |
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| Abstract | An 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. |
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| AbstractList | 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. An 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. ABSTRACTEmerging 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. 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. 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.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.An 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.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. 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 and , 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. An 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. 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. |
| Author | Brennan, Caitriona Chaumont, Soline Roeselers, Guus Cowart, Charles Laiola, Manolo Arteaga, Liliana McDonald, Daniel Oles, Renee Tribelhorn, Caitlin Khatib, Lora Knol, Jan Knight, Rob Sanders, Jon G. Litwin, Nicole Farmer, Sawyer Nizet, Oliver Bartko, Andrew Hernandez, Alejandra Rios Derrien, Muriel Das, Promi Myers, Tyler Shetty, Sudarshan A. Birmingham, Amanda Cotillard, Aurélie Tovar, Armando R. Bryant, Mackenzie Gilbert, Kat Koutnikova, Hana González, Antonio Lay, Christophe Diaz, Edgar A. Dilmore, Amanda H. Nowinski, Brent Sanders-Bodai, Karenina Torres, Nimbe Veiga, Patrick Tap, Julien Song, Se Jin |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/40586597$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1128/msystems.01378-21 10.1161/JAHA.119.012401 10.1038/s41587-020-00797-0 10.1093/ajcn/nqab332 10.1128/msystems.00167-22 10.1016/j.chom.2023.09.013 10.1128/mSystems.00016-19 10.1128/mSystems.00031-18 10.1038/s41522-021-00248-x 10.1093/femsre/fuad039 10.1016/j.cub.2020.09.063 10.1136/annrheumdis-2018-214514 10.1038/ismej.2017.126 10.1016/j.cmet.2015.10.001 10.1038/s41564-023-01388-w 10.1186/s40168-016-0202-1 10.1016/j.jand.2013.11.017 10.1017/S0007114510001030 10.1099/ijsem.0.005379 10.1007/s10096-012-1651-5 10.3390/nu13103459 |
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| Contributor | Cobo Díaz, José Francisco Chen, Lianmin |
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| Copyright | Copyright © 2025 Khatib et al. Copyright © 2025 Khatib et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Copyright © 2025 Khatib et al. 2025 Khatib et al. |
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| Keywords | Prevotella diet human microbiome metagenomics Faecalibacterium |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., has equity, and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant and scientific advisory board member for DayTwo and receives income. He has equity in and acts as a consultant for Cybele. He is a co‐founder of Biota, Inc., and has equity. He is a co-founder of Micronoma, has equity, and is a scientific advisory board member. The terms of this arrangement have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. A.B. is a founder of Guilden Corporation and is an equity owner. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. D.M. is a consultant for BiomeSense, Inc., has equity, and receives income. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict-of-interest policies. C.L., A.C., H.K., M.D., J.T., P.V., S.A.S., M.L., G.R., J.K., and S.C. are employees of Danone. |
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| Snippet | An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary... Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been... ABSTRACTEmerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts... ABSTRACT Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts... |
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| Title | A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population |
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