Fig. 4: Pathways with microbial enzymes differentiate the urban/rural metabolome and associate with cytokine responses.
From: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations
a The intensities of 1607 metabolites were standardized (z-scored) across the samples and projected with t-SNE. K-means cluster was used to discover 28 metabolite clusters (“Methods”) and annotated with the most prevalent HMDB molecular class. b t-SNE plot of samples metabolome profiles separating urban and rural samples. c Differentially abundant metabolites between urban and rural samples (Wilcoxon rank-sum two-sided test, PBonferroni < 0.05), stratified by KEGG pathways. d, e Number of positive and negative effects metabolites on cytokine expression, counted by detected KEGG pathways. Pathways with at least 10 different microbial enzymes in the entire cohort are selected. Metabolite-cytokine correlations are determined by Spearman correlation test subject to PFDR < 0.05. Source data are provided in the Source data file.
