Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis Timur Tuganbaev1,*, Uria Mor1,*, Stavros Bashiardes1, Timur Liwinski1,2, Samuel Philip Nobs1, Avner Leshem1, Mally Dori-Bachash1, Christoph A. Thaiss1,3, Elisha Y. Pinker1, Karina Ratiner1, Lorenz Kurt Adlung1, Sara Federici1, Christian Kleimeyer1, Claudia Moresi1, Takahiro Yamada4, Yotam Cohen1, Xiao Zhang5,6, Hassan Massalha7, Efi Massasa7, Yael Kuperman8, Pandelakis A. Koni9,10, Alon Harmelin8, Nan Gao5,6 Shalev Itzkovitz7, Kenya Honda11,12, Hagit Shapiro1,*, Eran Elinav1,13,14 1Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel 21st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 3Current address: Microbiology Department, Institute for Immunology, and Institute for Diabetes, Obesity & Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. 4Division of Biochemistry, Faculty of Pharmacy, Keio University, Tokyo, Japan 5Department of Biological Sciences, Rutgers University, Newark, NJ 07102, United States 6Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, United States 7Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel 8Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 7610001, Israel 9Georgia Cancer Center, Augusta University, Augusta, GA 30912, United States 10Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, United States 11RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan 12Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan 13Division of Cancer-Microbiome Research, DKFZ, Heidelberg, 69120, Germany 14Lead contact Throughout a 24-hour period, the small intestine (SI) is exposed to diurnally varying food- and microbiome-derived antigenic burdens, but maintains a strict immune homeostasis, which when perturbed in genetically-susceptible individuals, may lead to Crohn’s disease. Herein, we demonstrate that dietary content and rhythmicity regulate the diurnally-shifting SI epithelial cell (SIEC) transcriptional landscape, through modulation of the SI microbiome. We exemplify this concept with SIEC MHCII, which is diurnally modulated by distinct mucosal-adherent SI commensals, while supporting downstream circadian activity of intra-epithelial IL-10+ lymphocytes regulating SI barrier function. Disruption of this diurnally-regulated diet-microbiome-MHCII-IL10-epithelial barrier axis by circadian clock disarrangement, alterations in feeding time or content, or epithelial-specific MHCII depletion leads to an extensive microbial product influx, driving Crohn’s-like enteritis. Collectively, we highlight nutritional features that modulate SI microbiome, immunity, and barrier function, and identify dietary, epithelial and immune checkpoints along this axis to be potentially exploitable in future Crohn’s disease interventions.