(A) Treatment schema. ADFH B6N mice received 3AB cocktail water for 7 days followed by normal drinking water. Four days later, mice were gavaged with MHC-II suppressor bacteria (1:1 mix of B. thetaiotaomicron and C. sporogenes) or vehicle (culture media) for 2 weeks. Mice were then lethally irradiated (1000 cGy) and analyzed 24 hours later. (B) Quantification of % MHC-II expression and MFI on ileal IEC (n = 10 per group, combined with 2 independent experiments. Statistical analysis by T-test with Welch’s correction [mean ± SEM]). (C) Quantification of relative abundance of Clostridium and Bacteroides (genus) in cultured bacteria and fecal samples (n = 10 per group, combined with 2 independent experiments. Statistical analysis by Mann-Whitney test [mean ± SEM]). (D) Genus-rank relative abundance of fecal bacteria. (E) Genera that negatively (blue) or positively (orange) correlated with MHC-II expression. #p < 0.1 (unadjusted). (F) ADFH B6N male and female mice were treated as described in (A), then transplanted with female B6 BM and 0.5 x 106 Marilyn T cells. Survival by Kaplan-Meier analysis (n = 17 - 18 per male group combined from 2 independent experiments). *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. See also Figure S5 and S6.