Segmented filamentous bacteria prevent and cure rotavirus infection

Enteric viruses encounter epithelial cells amidst diverse microbiota. We thus hypothesized that our unintentional generation of rotavirus (RV)-resistant Rag1-KO mice reflected microbiota influencing RV infection. Accordingly, such RV-resistance was transferred by co-housing and fecal transplant. Interrogation of microbiotas conferring RV-resistance via antimicrobial agents, heat, and filtration, followed by limiting dilution transplant to germfree mice and subsequent fecal DNA sequencing revealed a central role for segmented filamentous bacteria (SFB), which was sufficient to protect mice against RV infection and associated diarrhea. Such protection was independent of lymphocytes (innate and adaptive), interferon, IL-17, and IL-22. Incubation of SFB-containing feces with RV reduced RV infectivity, suggesting direct disabling of this virus. Additionally, colonization of ileum by SFB induce changes in host gene expression and accelerated epithelial cell turnover, which can reduce RV burden. Thus, irrespective of its effects on immune cells, SFB confers protection against certain enteric viral infections and associated diarrheal disease.