Colitis Induction and Therapeutic Interventions in Mice

To induce colitis, mice were administered drinking water supplemented with 2% (wt./vol.) dextran sulfate sodium (DSS; MP Biomedicals, LLC, Aurora, OH, USA) for 7 d and were then allowed to recover by drinking unsupplemented water for the next 5 d (Supplementary Fig. 1a). The 6-formylindolo(3,2-b)carbazole (Ficz; Enzo Life Sciences, Lausen, Switzerland) and the AHR antagonist CH223191 (AHR⁻; Sigma-Aldrich) were resuspended in dimethyl sulfoxide (DMSO; Sigma-Aldrich) and administered intraperitoneally. Ficz was injected 1 d after DSS administration (1 μg/mouse). For the AHR⁻ treatment, WT→GF and Card9^−/−→GF mice (4- to 5-week-old females) were treated (100 μg/mouse) three times per week until euthanization (Fig. 5c). Controls consisted of mice injected with DMSO vehicle alone for the Ficz and AHR⁻ treatment groups. Three bacteria with strong AHR activity and that were isolated in feces of WT mice were identified by sequencing the 16S rDNA gene as previously described^{36 (link)}. The resulting sequences were aligned, inspected by eye, and compared with the online tool BLAST. Strains were identified based on the highest hit scores. These strains were deposited in the Collection Nationale de Cultures de Microorganismes (CNCM) of the Institut Pasteur and named L. murinus CNCM I-5020, L. reuteri CNCM I-5022, and L. taiwanensis CNCM I-5019. Bacterial suspensions containing these three strains (10⁹ colony-forming units (c.f.u.) of each strain in 500 μl of PBS) were administered three times per week for a period of 3 weeks to WT→GF and Card9^−/−→GF mice (4- to 5-week-old females) by intragastric gavage (Fig. 5c). Oral gavage with PBS was performed in control mice. For the antifungal treatment, mice were fed 0.5 mg/ml fluconazole in drinking water (Sigma-Aldrich) 1 week before DSS administration and every day thereafter, as previously described^{19 (link)} (Supplementary Fig. 6c). For the IL-22 treatment, WT and Card9^−/− mice were injected intraperitoneally three times per week with mouse IL-22–Fc (50 μg/mouse) (Genentech, South San Francisco, CA, USA) (WT IL-22 and Card9^−/− IL-22) or an equivalent amount of isotype control (IgG2a) (Genentech) (WT isotype and Card9^−/− isotype) for a period of 3 weeks. 3 d after the last injections, colitis was induced by DSS treatment (Supplementary Fig. 13c). In all treatments, body weight, blood in stool, and stool consistency were analyzed daily. The severity of colitis was assessed using the disease activity index (DAI) as previously described^{8 (link)}.