Genome-wide associations of human gut microbiota variation and implications for causal inference analyses

Here we use appropriate taxon-specific models along with support from independent cohorts to show association between human host genotype and gut microbiome variation. Using fecal derived 16S rRNA gene sequences and host genotype data from the Flemish Gut Flora Project (FGFP) we identify genetic associations involving multiple microbial traits. Mendelian randomization analysis was able to estimate associations between microbial traits and disease, however in the absence of clear microbiome driven effects, caution is needed in interpretation. This work marks a growing catalog of genetic associations which will provide insight into the contribution of host genotype to gut microbiome. Despite this, the uncertain origin of association signals will likely complicate future work looking to dissect function or use associations for causal inference analysis.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 5 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006141	16S sequencing data from 2259 Flemish Gut Flora Project (FGFP) samples	Illumina HiSeq 2500	2259

Publications	Citations
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Hughes DA, Bacigalupe R, Wang J, Rühlemann MC, Tito RY, Falony G, Joossens M, Vieira-Silva S, Henckaerts L, Rymenans L, Verspecht C, Ring S, Franke A, Wade KH, Timpson NJ, Raes J. Nat Microbiol 5: 2020 1079-1087	102
Large-scale association analyses identify host factors influencing human gut microbiome composition. Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Nat Genet 53: 2021 156-165	745
<i>Dysosmobacter welbionis</i> is a newly isolated human commensal bacterium preventing diet-induced obesity and metabolic disorders in mice. Le Roy T, Moens de Hase E, Van Hul M, Paquot A, Pelicaen R, Régnier M, Depommier C, Druart C, Everard A, Maiter D, Delzenne NM, Delzenne NM, Bindels LB, de Barsy M, Loumaye A, Hermans MP, Thissen JP, Vieira-Silva S, Falony G, Raes J, Muccioli GG, Cani PD. Gut 71: 2022 534-543	78
Transcriptome-wide association study identified candidate genes associated with gut microbiota. Pan C, Ning Y, Jia Y, Cheng S, Wen Y, Yang X, Meng P, Li C, Zhang H, Chen Y, Zhang J, Zhang Z, Zhang F. Gut Pathog 13: 2021 74	6
Assessing the relationship between gut microbiota and irritable bowel syndrome: a two-sample Mendelian randomization analysis. Liu B, Ye D, Yang H, Song J, Sun X, He Z, Mao Y, Hao G. BMC Gastroenterol 23: 2023 150	15