Fig. 2: Germline genetic variants and the gut metagenome affect transcriptional and phenotypic profiles of immune cells.

a, Number of significant independent eQTLs in each cell type of L1 and L2 levels. The bars are colored by cluster resolution (L1 or L2 level) and shaded by independence of eQTL mapping. DC, dendritic cell. b, Scatterplot depicting the correlation between median number of cells per sample and median effect size of significant eQTLs in each cell type. The x axis is on a log₁₀ scale. c, Number of significant eGenes shared among cell types in the L1 level. eGenes identified in only one cell type are colored pink, and those in multiple cell types are connected by lines and colored gray. d, Heatmap showing a pairwise comparison of eQTL effect size. Only significant eQTLs in one cell type (reference) that could be evaluated in other cell types (target) were analyzed. e, Heatmap depicting the enrichment of primary significant eQTLs of L2 cell types in promoter or enhancer regions of eight representative immune cells from the Roadmap project. f, Box plot showing the enrichment of primary eQTLs in promoters or enhancers of the corresponding cell types (n = 28) from the Roadmap project, according to effect sizes (Methods). g, Graphical representation of neighborhoods identified by Milo in healthy individuals (n = 131). Nodes are neighborhoods, colored by log₂ (fold change (FC)) by the relative abundance of R. gnavus adjusted for age, sex and sequencing groups. Sizes correspond to the number of cells in a neighborhood. Graph edges depict the number of cells shared between adjacent neighborhoods. Nhood, neighborhood. h, Beeswarm plot and box plot showing the distribution of adjusted log₂ (FC) in neighborhoods (n = 43,089) by the relative abundance of R. gnavus among L2 cell types. Colors are represented in the same way as in g. Boxes denote the interquartile range (IQR), medians are shown as horizontal bars, and whiskers extend to 1.5 times the IQR in f,h. N, naive; TCM, central memory T cell; TEM, effector memory T cell; CTL, cytotoxic T cell; N1, type 1 naive; N2, type 2 naive; IN, intermediate; Cyto, cytokine; Act, activated; corr, correlation.