RT Journal Article
SR Electronic
T1 The Dutch Microbiome Project defines factors that shape the healthy gut microbiome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.27.401125
DO 10.1101/2020.11.27.401125
A1 R. Gacesa
A1 A. Kurilshikov
A1 A. Vich Vila
A1 T. Sinha
A1 M.A.Y. Klaassen
A1 L.A. Bolte
A1 S. Andreu-Sánchez
A1 L. Chen
A1 V. Collij
A1 S. Hu
A1 J.A.M. Dekens
A1 V.C. Lenters
A1 J.R. Björk
A1 J.C. Swarte
A1 M.A. Swertz
A1 B.H. Jansen
A1 J. Gelderloos-Arends
A1 Lifelines cohort study
A1 M. Hofker
A1 R.C.H. Vermeulen
A1 S. Sanna
A1 H.J.M. Harmsen
A1 C. Wijmenga
A1 J. Fu
A1 A. Zhernakova
A1 R.K. Weersma
YR 2020
UL http://biorxiv.org/content/early/2020/11/27/2020.11.27.401125.abstract
AB The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only ∼13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.Competing Interest StatementThe authors have declared no competing interest.