fig3

Figure 3. Colonisation with E. lenta significantly changed metabolomes in the colon. PCA of all identified metabolite peaks detected in positive ionisation according to (A) colonisation, and (B) diet; (C) Annotated metabolites with significant differences between E.L and MM mice within at least one dietary group as measured in positive ionisation mode. Individual values for the metabolites in grey boxes are shown in panel (D). The symbols after metabolite names indicate those detected in the two ionisation modes and statistically significant in both (*) or only in the specific ionisation mode (#). The strength of significance is shown with a colour gradient (pale yellow to brown). The first coloured column indicates significance (adjusted P-values) according to multi-group comparisons (Kruskal-Wallis with Benjamini-Hochberg adjustment). The remaining columns indicate the results of Dunn’s test for post hoc comparisons between E.L and MM mice per diet. The grey arrows indicate the direction of changes as specified in the figure legend; (D) Peak intensity of the individual metabolites showing significant pairwise comparisons between the two colonisation groups in at least 3 of the 4 diets. Dots represent the values for individual mice; black bars indicate median values; within each group, mice housed in different cages are indicated with empty or filled circles. Statistics: **adj. P < 0.01, ****adj. P < 0.0001, Kruskal-Wallis; for each metabolite, different letters indicate significance between the corresponding groups (Dunn’s test); (E-H) Same as in panels (A-D) for the negative ionisation mode. PCA: Principal component analysis; E.L: mice colonised with OMM12 and Coriobacteriia; MM: mice colonised with the mouse synthetic community OMM12; CD: control diet; CD-BA: control diet supplemented with 0.2% primary bile acids; HFD: lard-based high-fat diet; HFD-BA: HFD supplemented with 0.2% primary bile acids; OMM12: Oligo-Mouse Microbiota.