Fig. 1. Bacterial production of MAIT ligands in the colonic mucosa.
(A) activation of MR1:5-OP-RU–specific TCR Tg T cells after coculture with WT3 or WT3-MR1 cells pulsed with colon luminal contents at the indicated dilutions (n = 3 mice per group; data pooled from N = 2). *P < 0.05, **P < 0.01, and ***P < 0.001 by unpaired multiple t tests with a false discovery rate (FDR) = 1%. UD, undiluted. (B) left, MR1:5-OP-RU–specific TCR Tg T cell activation after coculture with WT3-MR1 cells pulsed with filtered luminal contents from control or antibiotic-treated mice. Right, MAIT ligand concentrations expressed as 5-OP-RU equivalent (n = 3 to 5 mice per group; representative of N = 2). the dotted line indicates TCR Tg T cell activation in the absence of intestinal contents. *P < 0.05 by unpaired multiple Mann-Whitney U tests with an FDR = 1%. (C) Estimation of cecal bacterial numbers by qPcR amplification of the 16S rRna gene (data pooled from N = 2). *P < 0.05 by paired Wilcoxon test. (D) top, MR1:5-OP-RU–specific TCR Tg T cell activation after coculture with WT3-MR1 cells pulsed with lumen or mucosal cecal contents. Bottom left, relative expression of CD25 and CD69 by MR1:5-OP-RU–specific TCR Tg T cells in the indicated conditions (means ± SEMs, n = 9 or 10 mice; data pooled from N = 2). **P < 0.01 by paired multiple t tests with an FDR = 1%. Bottom right: Mait ligand concentrations expressed as 5-OP-RU equivalent. **P < 0.01 by paired Wilcoxon test. (E) abundance of the indicated phyla in the cecum. columns indicate individual mice. (F) Differentially expressed metabolic pathways between the lumen and mucosal bacterial communities [Padj < 0.001 by Mann-Whitney U test, log fold change (LFC) > 0.5]. (G) top, riboflavin biosynthetic pathway gene expression in the cecal lumen and mucosa (Padj ≤ 0.05 by Mann-Whitney U test). Bottom, scheme of the riboflavin biosynthesis pathway. (H) taxonomy of total (left) and ribD (right) bacterial transcripts in the lumen and mucosa. (I) Species-level taxonomy of ribD transcripts in the lumen and mucosa.