Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Francesco Asnicar, Sarah Berry, Ana M. Valdes, Long Hoang Nguyen, Gianmarco Piccinno, David A Drew, Emily Leeming, Rachel Gibson, Haya Al Khatib, Lucy Francis, Mohsen Mazidi, Olatz Mompeo Masachs, Mireia Valles-Colomer, Adrian Tett, Francesco Beghini, Leonard Dubois, David Bazzani, Andrew Maltez Thomas, Chloe Mirzayi, Asya KhleborodovaSehyun Oh, Rachel Hine, Christopher Bonnett, Joan Capdevila, Serge Danzanvilliers, Francesca Giordano, Ludwig Geistlinger, Levi Waldron, Richard Davies, George Hadjigeorgiou, Jonathan Wolf, José María Ordovás, Christopher Gardner, Paul W. Franks, Andrew T Chan, Curtis Huttenhower, Tim Spector, Nicola Segata

Research output: Contribution to journalArticlepeer-review

425 Citations (Scopus)


The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.
Original languageEnglish
Pages (from-to)321-332
Number of pages12
JournalNature Medicine
Issue number2
Publication statusPublished - Feb 2021


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