Fig. 4

Colonization of germ-free mice with Clostridia induces a shift in the cecal metabolome. Comparative analysis of the cecal metabolome of germ-free mice (n = 6), gnotobiotic mice associated with a defined microbial community containing14 human Clostridia and 3 human Erysipelotrichia isolates (CE17) (n = 6), and gnotobiotic mice receiving a cecal microbiota transplant from conventional C57BL/6 J mice (C57FMT) (n = 4). a Principle component analysis of the cecal metabolome in the indicated groups of mice. b Bar plot of significantly increased and decreased metabolites by metabolite class in gnotobiotic mice associated with a defined microbial community (CE17) relative to germ-free mice (FDR corrected P value ≤ 0.05). c Volcano plot of metabolites colored by class. Metabolites with a positive fold-change value increased in mice engrafted with a defined microbial community compared to germ-free mice, while metabolites with a negative fold-change value decreased. The dashed line is set at an FDR corrected P value of 0.05. d Bar plot of significantly increased and decreased carbohydrates by metabolite subclass in gnotobiotic mice associated with a defined microbial community (CE17) relative to germ-free mice (FDR corrected P value ≤ 0.05). e Volcano plot of metabolites colored by class. Metabolites with a positive fold-change value increased in mice engrafted with a defined microbial community compared to gnotobiotic mice receiving a cecal microbiota transplant from conventional C57BL/6 J mice (C57FMT), while metabolites with a negative fold-change value decreased. f Bar plot of significantly increased and decreased metabolites by metabolite class in gnotobiotic mice associated with a defined microbial community (CE17) relative to gnotobiotic mice receiving a cecal microbiota transplant from conventional C57BL/6 J mice (C57FMT) (FDR corrected P value ≤ 0.05)