TY - JOUR
T1 - Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
AU - Asnicar, Francesco
AU - Berry, Sarah
AU - Valdes, Ana M.
AU - Nguyen, Long Hoang
AU - Piccinno, Gianmarco
AU - Drew, David A
AU - Leeming, Emily
AU - Gibson, Rachel
AU - Al Khatib, Haya
AU - Francis, Lucy
AU - Mazidi, Mohsen
AU - Mompeo Masachs, Olatz
AU - Valles-Colomer, Mireia
AU - Tett, Adrian
AU - Beghini, Francesco
AU - Dubois, Leonard
AU - Bazzani, David
AU - Maltez Thomas, Andrew
AU - Mirzayi, Chloe
AU - Khleborodova, Asya
AU - Oh, Sehyun
AU - Hine, Rachel
AU - Bonnett, Christopher
AU - Capdevila, Joan
AU - Danzanvilliers, Serge
AU - Giordano, Francesca
AU - Geistlinger, Ludwig
AU - Waldron, Levi
AU - Davies, Richard
AU - Hadjigeorgiou, George
AU - Wolf, Jonathan
AU - Ordovás, José María
AU - Gardner, Christopher
AU - Franks, Paul W.
AU - Chan, Andrew T
AU - Huttenhower, Curtis
AU - Spector, Tim
AU - Segata, Nicola
N1 - Funding Information:
We thank the participants of the PREDICT 1 study. We thank N. Atabaki-Pasdar for generating the liver fat score. We thank the staff of Zoe Global, the Department of Twin Research and the Massachusetts General Hospital and all the members of the Segata, Berry and Spector laboratories for their tireless work in contributing to the running of the study, data collection and data processing. We thank Nightingale Health and Affinity Biomarker Laboratories for their support and analytical work. This work was supported by Zoe Global and received support from grants from the Wellcome Trust (no. 212904/Z/18/Z) and Medical Research Council/British Heart Foundation Ancestry and Biological Informative Markers for Stratification of Hypertension (no. MR/M016560/1). The work was also supported by the European Research Council (ERC-STG project MetaPG-716575 to N.S.), MIUR ‘Futuro in Ricerca’ (grant no. RBFR13EWWI_001 to N.S.), the European H2020 program (ONCOBIOME-825410 and MASTER-818368 projects to N.S.), the National Cancer Institute of the National Institutes of Health (grant no. 1U01CA230551 to N.S.) and the Premio Internazionale Lombardia e Ricerca 2019 to N.S. S.E.B. was supported in part by a grant funded by the Biotechnology and Biological Sciences Research Council (grant no. BB/NO12739/1). P.W.F. was supported in part by grants from the European Research Council (grant no. CoG-2015_681742_NASCENT), Swedish Research Council (grant no. IRC15-0067) and Novo Nordisk Foundation. A.T.C. was supported in part as a Stuart and Suzanne Steele MGH Research Scholar. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation, Zoe Global and the National Institute for Health Research-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/2
Y1 - 2021/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85100135155&partnerID=8YFLogxK
U2 - https://doi.org/10.1038/s41591-020-01183-8
DO - https://doi.org/10.1038/s41591-020-01183-8
M3 - Article
SN - 1546-170X
VL - 27
SP - 321
EP - 332
JO - Nature Medicine
JF - Nature Medicine
IS - 2
ER -