biostudies-literatureBraun TEuropean Research CouncilNIDDK NIH HHS3764https://www.ebi.ac.uk/biostudies/studies/S-EPMC11069498biostudies-literatureUnknown15(1)Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene exNature communicationsDiet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort.PMC11069498R01 DK125296758313P30 DK078392Mao RAmir ABraun TAlgavi YKalter-Leibovici OPicard OMalik ADenson LAgranovich BLevhar NYavzori MZhuo SToren IStappenbeck TSEfroni GChen MHaberman YBorenstein EGottlieb EBen-Horin SAbu-Saad KShacham HLiu TCHadar RFeng RElinav EfalseDiet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort.Crohn disease (CD) burden has increased with globalization/urbanization, and the rapid rise is attributed to environmental changes rather than genetic drift. The Study Of Urban and Rural CD Evolution (SOURCE, n = 380) has considered diet-omics domains simultaneously to detect complex interactions and identify potential beneficial and pathogenic factors linked with rural-urban transition and CD. We characterize exposures, diet, ileal transcriptomics, metabolomics, and microbiome in newly diagnosed CD patients and controls in rural and urban China and Israel. We show that time spent by rural residents in urban environments is linked with changes in gut microbial composition and metabolomics, which mirror those seen in CD. Ileal transcriptomics highlights personal metabolic and immune gene ex2024-01-01T00:00:00Z2024 May2026-05-29T11:24:00.995Z2026-04-08T04:30:30.678ZS-EPMC110694983870436110.1038/s41467-024-48106-6