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Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort

Author

Listed:
  • Tzipi Braun

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Rui Feng

    (Sun Yat-Sen University
    Sun Yat-Sen University)

  • Amnon Amir

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Nina Levhar

    (Tel-Hashomer, Affiliated with the Tel Aviv University
    Tel Aviv University)

  • Hila Shacham

    (Tel-Hashomer, Affiliated with the Tel Aviv University
    Tel Aviv University)

  • Ren Mao

    (Sun Yat-Sen University)

  • Rotem Hadar

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Itamar Toren

    (Tel-Hashomer, Affiliated with the Tel Aviv University
    Hebrew University of Jerusalem)

  • Yadid Algavi

    (Tel Aviv University)

  • Kathleen Abu-Saad

    (Gertner Institute for Epidemiology and Health Policy Research)

  • Shuoyu Zhuo

    (Sun Yat-Sen University)

  • Gilat Efroni

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Alona Malik

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Orit Picard

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Miri Yavzori

    (Tel-Hashomer, Affiliated with the Tel Aviv University)

  • Bella Agranovich

    (Bat Galim)

  • Ta-Chiang Liu

    (Washington University in St Louis School of Medicine)

  • Thaddeus S. Stappenbeck

    (Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic)

  • Lee Denson

    (University of Cincinnati College of Medicine)

  • Ofra Kalter-Leibovici

    (Tel Aviv University
    Gertner Institute for Epidemiology and Health Policy Research)

  • Eyal Gottlieb

    (Bat Galim)

  • Elhanan Borenstein

    (Tel Aviv University
    Tel Aviv University
    Santa Fe Institute)

  • Eran Elinav

    (Weizmann Institute of Science
    German National Cancer Center (DKFZ))

  • Minhu Chen

    (Sun Yat-Sen University)

  • Shomron Ben-Horin

    (Tel-Hashomer, Affiliated with the Tel Aviv University
    Tel Aviv University)

  • Yael Haberman

    (Tel-Hashomer, Affiliated with the Tel Aviv University
    Tel Aviv University
    University of Cincinnati College of Medicine)

Abstract

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 expression modules, that are directly linked to potential protective dietary exposures (coffee, manganese, vitamin D), fecal metabolites, and the microbiome. Bacteria-associated metabolites are primarily linked with host immune modules, whereas diet-linked metabolites are associated with host epithelial metabolic functions.

Suggested Citation

  • Tzipi Braun & Rui Feng & Amnon Amir & Nina Levhar & Hila Shacham & Ren Mao & Rotem Hadar & Itamar Toren & Yadid Algavi & Kathleen Abu-Saad & Shuoyu Zhuo & Gilat Efroni & Alona Malik & Orit Picard & Mi, 2024. "Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48106-6
    DOI: 10.1038/s41467-024-48106-6
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    References listed on IDEAS

    as
    1. Yael Haberman & Rebekah Karns & Phillip J. Dexheimer & Melanie Schirmer & Judith Somekh & Ingrid Jurickova & Tzipi Braun & Elizabeth Novak & Laura Bauman & Margaret H. Collins & Angela Mo & Michael J., 2019. "Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    2. Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Je, 2021. "Multivariable association discovery in population-scale meta-omics studies," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-27, November.
    3. Walid Mottawea & Cheng-Kang Chiang & Marcus Mühlbauer & Amanda E. Starr & James Butcher & Turki Abujamel & Shelley A. Deeke & Annette Brandel & Hu Zhou & Shadi Shokralla & Mehrdad Hajibabaei & Ruth Si, 2016. "Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease," Nature Communications, Nature, vol. 7(1), pages 1-14, December.
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