Large-scale association analyses identify host factors influencing human gut microbiome composition

A Kurilshikov, Maria Medina Gomez, R Bacigalupe, Djawad Radjabzadeh, J Wang, A Demirkan, CI Le Roy, JAR Garay, CT Finnicum, XR Liu, DV Zhernakova, MJ Bonder, TH Hansen, F Frost, MC Ruhlemann, W Turpin, JY Moon, HN Kim, K Lull, E BarkanSA Shah, M Fornage, J Szopinska-Tokov, ZD Wallen, D Borisevich, L Agreus, A Andreasson, C Bang, L Bedrani, JT Bell, H Bisgaard, M Boehnke, DI Boomsma, RD Burk, A Claringbould, K Croitoru, GE Davies, Cornelia Duijn, Liesbeth Duijts, G Falony, JY Fu, A Graaf, T Hansen, G Homuth, DA Hughes, RG Ijzerman, Matthew O. Jackson, Vincent Jaddoe, M Joossens, T Jorgensen, D Keszthelyi, R Knight, M Laakso, M Laudes, LJ Launer, W Lieb, AJ Lusis, AAM Masclee, Henriette Moll, Z Mujagic, Q Qibin, D Rothschild, H Shin, SJ Sorensen, CJ Steves, J Thorsen, NJ Timpson, RY Tito, S Vieira-Silva, U Volker, H Volzke, U Vosa, KH Wade, S Walter, K Watanabe, S Weiss, FU Weiss, O Weissbrod, HJ Westra, G Willemsen, H Payami, D Jonkers, AA Vasquez, EJCN de Geus, KA Meyer, J Stokholm, E Segal, E Org, C Wijmenga, HL Kim, RC Kaplan, TD Spector, André Uitterlinden, Fernando Rivadeneira, A Franke, MM Lerch, L Franke, S Sanna, M D'Amato, O Pedersen, AD Paterson, Robert Kraaij, J Raes, A Zhernakova

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372 Citations (Scopus)


To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10−8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10−20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10−10 < P < 5 × 10−8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.

Original languageEnglish
Pages (from-to)156-165
Number of pages10
JournalNature Genetics
Issue number2
Publication statusPublished - Feb 2021

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© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.


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