Fig. 4. Intestinal microbiota sustains the expression of a Carinh/IRF1 feedforward loop to maintain microbial homeostasis.

a, b qPCR analysis of Carinh, Irf1 and Reg3γ mRNA expression in the intestine from SPF and GF mice (a) (n = 4 mice per group), or from ABx-treated and untreated mice (b) (Ctrl n = 3 mice, ABx n = 4 mice). c, d qPCR analysis of Carinh and Irf1 mRNA levels in Carinh^KO BMDMs (c), Irf1^KO BMDMs (d), and their littermate controls in response to LPS stimulation with time-course. n = 4 per group. e Fecal 16S rDNA sequencing results for Carinh^KO mice and their littermates. PCoA plot generated from unweighted UniFrac distance matrix displaying the distinct clustering pattern for the intestinal bacteria communities of Carinh^KO mice and their littermates. f Relative abundance of taxonomic groups averaged across Carinh^KO mice and their littermates at the family level. g Composition differences of the intestinal microbiota in Carinh^KO mice and their littermates, determined by linear discriminant analysis using LEfSe. h–k DSS induced colitis model in ABx-treated or untreated Carinh^KO mice and their littermates. Colitis was monitored by body weight loss (h), colon shortening (i), and H&E staining of colon tissues (j, k). j Representative pictures. Scale bars, 50 μm. k Quantification of corresponding histology scores. 5 views per mice, 6 mice per group. l Fecal microbiota from Carinh^WT and Carinh^KO mice were transferred into ABx-treated WT recipients. And then colitis was induced by DSS in the FMT recipient mice. m–o Colitis was monitored by body weight loss (m), colon shortening (n), and H&E staining of colon tissues (o). For H&E staining (o): left, representative pictures. Scale bars, 50 μm. Right, quantification of corresponding histology scores. 5 views per mice, 9 mice per group. 6 pairs of Carinh^WT and Carinh^KO mice were used in 16S rDNA sequencing experiments shown in e–g and were representative of two independent 16S rDNA sequencing experiments. Data in i, j, n and o are representatives of three independent experiments. Body weight data in h and m are pooled from two independent experiments. Data in a–d are representative of at least three independent experiments. Data represent means ± SEM. Body weight changes (h and m) were analyzed by two-way ANOVA. Colon length (i) and histology scores (k) were analyzed by one-way ANOVA. Unpaired two-tailed Student’s t-tests were used for other statistical analyses. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; ns, not significant.