RAG1 and infection: Despite cohabitation and continuous microbial exposure from FMT-treated C57BL/6 mice, FMT-treated Rag1−/− mice exhibited significantly higher C. difficile burden (Supplementary Fig. 2B, D) and toxin titers in the feces (Supplementary Fig. 2C, E) compared to C57BL/6 mice in the context of either a CD196 strain infection (Supplementary Fig. 2B, C) or VPI10463 strain infection (Supplementary Fig. 2D, E).