We thank the members of the Elinav and Segal laboratories, and members of the DKFZ cancer-microbiome division for discussions, and apologize to authors whose work was not included owing to space constraints. We thank R. Straussman, D. Nejman and E. Hornstein for suggestions and help with experimental methodologies; C. Bar-Nathan for assistance with animal work; S. Belkin for providing reagents and A. Godneva for computational assistance. We thank J. Suez and N. Zmora for extensive editing during production. E.B. is supported by the Weizmann Institute Dean of Faculty fellowship. D.R. received a Levi Eshkol PhD Scholarship for Personalized Medicine by the Israeli Ministry of Science. N.Z. is supported by the Gilead Sciences International Research Scholars Program in Liver Disease. C.K. is supported by an MD fellowship of the Boehringer Ingelheim Fonds. Y.K. is the incumbent of the Sarah and Rolando Uziel Research Associate Chair. H.S. is the Incumbent of the Vera Rosenberg Schwartz Research Fellow Chair. E.S. is supported by the Crown Human Genome Center; the Else Kroener Fresenius Foundation; Donald L. Schwarz, Sherman Oaks, CA; Jack N. Halpern, NeNY; Leesa Steinberg, Canada; and grants funded by the European Research Council and the Israel Science Foundation. E.E. is supported by Y. and R. Ungar; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Gurwin Family Fund for Scientific Research; the Leona M. and Harry B. Helmsley Charitable Trust; the Crown Endowment Fund for Immunological Research; the Else Kroener Fresenius Foundation; the estate of J. Gitlitz; the estate of L. Hershkovich; the Benoziyo Endowment Fund for the Advancement of Science; the Adelis Foundation; J. L. and V. Schwartz; A. and G. Markovitz; A. and C. Adelson; the French National Center for Scientific Research (CNRS); D. L. Schwarz; The V. R. Schwartz Research Fellow Chair; L. Steinberg; J. N. Halpern; A. Edelheit; and by grants funded by the European Research Council, the Israel Science Foundation and the Helmholtz Foundation. E.E. is the Sir Marc and Lady Tania Feldmann Professorial Chair in Immunology, Weizmann Institute of Science, Israel; is the Director of the Microbiome Research Division, DKFZ, Heidelberg, Germany; is a senior fellow of the Canadian Institute of Advanced Research (CIFAR) and is an international scholar of The Bill and Melinda Gates Foundation and Howard Hughes Medical Institute (HHMI).