Fig. 2

Microbial species associated with gut microbial gene richness. a Nonmetric multidimensional scaling plot based on Bray–Curtis microbiome distances showing more different microbiome configurations in subjects with LGCs than in HGCs. Dot sizes are proportional to microbiome gene richness. Ellipses represent 95% confidence intervals. Microbial species associated to an environmental vector of more than 0.35 NMDS coordinate length are shown. b Microbial species positively (green) and negatively (red) correlated with gene richness (Benjamini–Hochberg corrected Spearman Rank correlation p value < 0.05) in MSM (n = 100) and non-MSM (n = 56) subjects. Most microbial species positively correlated with richness were GRAM-positive, whereas most species negatively correlated with richness were GRAM-negative (V is for “variable” GRAM staining). Blue squares on the left handside summarize some of the main microbial metabolism products of each species, including the short-chain fatty acids (SCFAs) acetate (Ace), butyrate (But), formate (For), and propionate (Pro); the acids lactate (Lac) and succinate (Suc); the gas methane (CH4), and the alcohols ethanol (Eth) and methanol (Met); * is for unknown. c Random forest analysis showing the contribution of each microbial species to overall gene richness. In green, red, and gray, respectively, microbial species enriched in HGCs, LGCs and not significantly enriched in either category. AUC area under the curve