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

doi:10.1038/s41564-020-0743-8

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Nat Microbiol. Author manuscript; available in PMC 2021 Mar 29.

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Nat Microbiol. 2020 Sep 1; 5(9): 1079–1087.

Published online 2020 Jun 22. doi: 10.1038/s41564-020-0743-8

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Table 1

Meta-supported genetic variants.

Taxon	Model	rsID	SNP ID	Chromosome	Position (bp)	EAF	β	se	p-value	N	Q	hetP	I²	Closest gene
G_Ruminococcus	P/A	rs150018970	9:134648925_G_A	9	134,648,925	0.010	0.111	0.294	6.68×10^-14	3890	10.763	0.005	81.417	RAPGEF1
G_Coprococcus	P/A	rs561177583	1:96741622_G_A	1	96,741,622	0.012	0.161	0.283	1.10×10^-10	3890	22.036	0.000	90.924	NA
G_Butyricicoccus	AB	rs55808472	16:24931691_G_A	16	24,931,691	0.073	0.257	0.041	5.54 x10^-10	3890	1.248	0.536	0.000	ARHGAP17
F_Sutterellaceae	P/A	rs4494297	11:44145588_G_T	11	44,145,588	0.011	0.144	0.314	6.80 x10^-10	3890	3.478	0.176	42.497	EXT2
G_Dialister	P/A	rs7118902	11:121440231_G_A	11	121,440,231	0.306	0.734	0.053	4.14 x10^-09	3890	0.684	0.710	0.000	SORL1
G_u_F_Porphyromonadaceae	AB	rs35980751	13:96011248_G_T	13	96,011,248	0.259	0.196	0.034	5.07 x10^-09	2094	1.090	0.580	0.000	ABCC4
G_Parabacteroides	AB	rs13207588	6:41519430_G_A	6	41,519,430	0.229	-0.180	0.031	6.89 x10^-09	3890	5.120	0.077	60.938	FOXP4
G_u_F_Erysipelotrichaceae	P/A	rs6733298	2:56450856_A_G	2	56,450,856	0.891	1.640	0.085	6.91 x10^-09	3890	1.739	0.419	0.000	CCDC85A
C_Gammaproteobacteria	AB	rs116865000	15:95639861_G_A	15	95,639,861	0.025	0.555	0.096	8.41 x10^-09	3213	1.847	0.397	0.000	NA
G_u_P_Firmicutes	AB	rs11788336	9:111688387_T_C	9	111,688,387	0.273	-0.143	0.025	1.66 x10^-08	3485	5.388	0.068	62.882	IKBKAP
G_u_P_Firmicutes	P/A	rs34656657	6:16613223_G_A	6	16,613,223	0.022	0.294	0.218	1.82 x10^-08	3890	2.845	0.241	29.710	ATXN1
G_u_O_Bacteroidales	P/A	rs116135844	4:168179343_G_A	4	168,179,343	0.043	2.109	0.134	2.32 x10^-08	3890	1.969	0.374	0.000	SPOCK3
G_Veillonella	P/A	rs117338748	15:58714239_G_A	15	58,714,239	0.019	2.887	0.190	2.42 x10^-08	3890	2.109	0.348	5.178	LIPC

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Genetic variants, representing LD-tagged loci, associated with 16S gut microbiome phenotypes at a meta-p-value smaller than 2.5×10^-08. Presented are the microbial taxa, the trait model type - abundance (AB) or presence/absence (P/A) - the reference SNP identifier (rsID), the SNP ID composed of chromosome, base pair (build hg19), alternative allele and effect allele, chromosome, position (bp), the effect allele frequency (EAF), the meta estimated effect size (β; presented as odds ratios for P/A, and in SD units of change for AB outcomes), standard error (se, in log(OR) scale for P/A outcomes), two-sided inverse variance fixed effect meta p-value, meta-sample size (N), Cochran’s Q heterogeneity statistic (Q), the heterogeneity p-value (hetP), the proportion of variation among studies due to heterogeneity (I2) and the physically closest gene (+/- 250kb). P, C, O, F, G preceding taxa names indicate the classification levels phylum, class, order, family and genus, while u indicates unclassified. Genetic variants are sorted by significance (p-value), with the top two surpassing the study-wide meta-analysis p-value shaded in blue. Taxon names include abbreviated taxonomic levels, where “G” represents genus, “F” family, “O” order, “P” phylum, and “u” unclassified.