Fig. 1

Comparative analysis of the gut microbiota in independent animal units. a Box and whisker plot of the alpha diversity indices for richness (Chao1 and observed OTUs indices) and evenness (Shannon index) of the bacterial communities in TSHR-immunized mice housed in Center 1 (blue) and Center 2 (red), respectively. Tukey’s HSD post hoc: Chao1, P = 0.01; observed OTUs, P < 0.001; Shannon, P = 0.08. b Annotated heatmap based on Spearman distance and Ward hierarchical clustering of the top 30 genera shows how well the two locations cluster together. Taxonomy explanation includes genera, family, and phylum, which are entered in order of abundance. Genus abundance is described by the change in the intensity of the gray color, as annotated. c Multidimensional scaling plot (MDS) based on the weighted Unifrac distances between the two animal units. PERMANOVA with 999 permutations P = 0.005. d Differentially abundant family from a pairwise comparison with Welch’s t test with 95% confidence intervals (STAMP). e Box and whisker plot culture results from intestinal scraped samples derived from TSHR-immunized mice from Center 1 and Center 2. Results are expressed as a Log(x + 1) transformed colony-forming units/gram feces (cfu/g). P values: * P < 0.05; ** P < 0.001; *** P < 0.005