Fig. 2.

Gut microbiota composition in TSHR-immunized mice and control mice in Center 2 at final timepoint. a Box and whisker plots describing the measurement of alpha diversity (Chao, ACE, and Shannon indices). b Non-metric dimensional scaling (NMDS) plot of weighted Unifrac distances showed a spatial separation of microbial communities according to the immunizations. PERMANOVA based on 999 permutations P = 0.001. c Boxplot of the phylum counts according to immunizations. ANOVA on phylum counts BH adjusted P < 0.0001 and pairwise T test between Bacteroidetes-Firmicutes counts adjusted P = 0.0003. d Non-Metric Dimensional Scaling (NMDS) plot based on weighted Unifrac distances shows spatial separation of the microbial community according to the immunization and caging within Center 2. Mice were co-housed according to their immunization at a maximum of four animals; cages are described by different shapes as in the legend. No significant difference in cage effect is observed. PERMANOVA based on cage effect (999 permutations) for all comparisons P = 0.12. P values: * P ≤ 0.05; ** P = 0.01