We thank members of the Sonnenberg Laboratory for discussions and critical reading of the manuscript, and T. Shima and Y. Umesaki from Yakult Central Institute for providing segmented filamentous bacteria and advice. Research in the Sonnenberg Laboratory is supported by the National Institutes of Health (R01AI143842, R01AI123368, R01AI145989, R21DK110262 and U01AI095608), the NIAID Mucosal Immunology Studies Team (MIST), the Crohn’s and Colitis Foundation, the Searle Scholars Program, the American Asthma Foundation Scholar Award, Pilot Project Funding from the Center for Advanced Digestive Care (CADC), an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund, a Wade F. B. Thompson/Cancer Research Institute CLIP Investigator grant, the Meyer Cancer Center Collaborative Research Initiative and the Jill Roberts Institute (JRI) for Research in IBD. L.Z. and J.G. are supported by fellowships from the Crohn’s and Colitis Foundation (608975 and 519428). N.J.B. is supported by a fellowship from the NIH (F32AI124517). We thank the Epigenomics Core of Weill Cornell Medicine, and all contributing members of the JRI IBD Live Cell Bank, which is supported by the JRI, Jill Roberts Center for IBD, Cure for IBD, the Rosanne H. Silbermann Foundation and Weill Cornell Medicine Division of Pediatric Gastroenterology and Nutrition. Research in the Vivier laboratory is supported by funding form the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (TILC, grant agreement no. 694502); the Agence Nationale de la Recherche; Equipe Labellisée ‘La Ligue’, Ligue Nationale contre le Cancer, MSDAvenir, Innate Pharma and institutional grants to the CIML (INSERM, CNRS and Aix-Marseille University) and to Marseille Immunopôle. Research reported in this publication was supported by the National Center for Advancing Translational Science of the National Institute of Health, under award number UL1TR002384.

Reviewer information

Nature thanks Koji Hase, Scott Snapper and the other anonymous reviewer(s) for their contribution to the peer review of this work.