(a) LocusZoom plot of adjusted effect size (for each SNP, the actual effect size is divided by the significance threshold adjusted according to MAF category, represented by the dashed line; Online Methods) at the VDR locus, where two SNPs passed the significance threshold for association with β diversity (P < 5 × 10−8 for association with overall microbiome variation, measured by BC). (b) Association between genotypes at the lead SNP (rs7974353) and β diversity (BC). Microbiome data are shown in a PCoA plot; the dashed lines contain 50% of the samples for each group (for visualization) and show differences in the centroids for each genotype group; n = 1,812. (c) Meta-analysis in humans shows Parabacteroides to be the most significant taxon correlated with VDR using a GLM (Online Methods). The x axis shows the percentage of nonzero values for each genotype at rs7974353, and boxes and bars summarize 50% and 95% confidence intervals, respectively, for nonzero values; n = 1,812. (d) Knockout of Vdr in mice also leads to changes in Parabacteroides abundance. Error bars, 5–95% confidence intervals (n = 3 wild-type (WT) mice and n = 5 knockout mice; ). (e) LocusZoom plot for adjusted effect size in the region upstream of POMC, where 78 SNPs passed the significance threshold. (f) Association between the genotypes of the lead SNP at POMC (rs72853661) and β diversity (BC). Microbiome data are shown in a PCoA plot; the dashed lines contain 50% of the samples for each group (for visualization) and show differences in the centroids for each genotype group; n = 1,812.