Extended Data Fig. 3. Colonic microbial profiling of rich-diet mice versus minimal-diet mice.

(a-d) Three-week-old SPF mice were fed a nutrient-rich diet or a minimal diet, and the microbial compositions in colonic lumen were analyzed after 4 weeks by 16S rRNA sequencing. Observed OTUs (a), Shannon index (b), PCoA analysis (c), and relative abundance of bacteria at the phylum and family levels (d) are shown. (e) Quantitative PCR analysis of 16S rDNA of Clostridium cluster IV and Clostridium cluster XIVα in colonic luminal specimens from SPF mice fed a nutrient-rich diet, a minimal diet, or a minimal diet supplemented with the indicated primary BAs (CA/CDCA/UDCA, 2 mM of each) or secondary BAs (Oxo-BAs/LCA/DCA, 1 mM of each) in drinking water. (f) Four-week-old GF mice or GF mice receiving transferred fecal materials (FMT) from minimal-diet or rich-diet SPF mice were fed a nutrient-rich diet or a minimal diet, and colonic Tregs were analyzed after 2 weeks. Frequencies of colonic RORγ⁺Helios^– in the Foxp3⁺CD4⁺TCRβ⁺ Treg population are shown. Data are pooled from three independent experiments in a-d. Data are representative of two independent experiments in e, f. n represents biologically independent animals. Bars indicate mean ± SEM value, and ∗∗∗p < 0.001 in one-way analysis of variance followed by the Bonferroni post hoc test.