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

Tzipi Braun; Rui Feng; Amnon Amir; Nina Levhar; Hila Shacham; Ren Mao; Itamar Toren; Kathleen Abu-Saad; Shuoyu Zhuo; Gilat Efroni; Alona Malik; Orit Picard; Miri Yavzori; Bella Agranovich; Ta Chiang Liu; Thaddeus S. Stappenbeck; Lee Denson; Ofra Kalter-Leibovici; Eyal Gottlieb; Elhanan Borenstein; Eran Elinav; Minhu Chen; Shomron Ben-Horin; Yael Haberman

doi:10.1038/s41467-024-48106-6

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

Tzipi Braun, Rui Feng, Amnon Amir, Nina Levhar, Hila Shacham, Ren Mao, Itamar Toren, Kathleen Abu-Saad, Shuoyu Zhuo, Gilat Efroni, Alona Malik, Orit Picard, Miri Yavzori, Bella Agranovich, Ta Chiang Liu, Thaddeus S. Stappenbeck, Lee Denson, Ofra Kalter-Leibovici, Eyal Gottlieb, Elhanan BorensteinEran Elinav, Minhu Chen, Shomron Ben-Horin, Yael Haberman^*

^*Corresponding author for this work

Department of Systems Immunology

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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.

Original language	English
Article number	3764
Journal	Nature Communications
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-48106-6
Publication status	Published - 4 May 2024

Bibliographical note

We thank all study participants. Support for the SOURCE study was provided by the Helmsley Charitable Trust (E.E., S.B.H., Y.H.). Other support included the ERC starting grant (Y.H., grant No. 758313), Tel Aviv University’s Colton Center for Autoimmune Diseases (E.B., Y.H.), the Israel Science Foundation (Y.H., grant No. 785/22), the I-CORE program (Y.H., grants No. 41/11), Israel Science, Culture, and Sport (Y.H., grant no. 4361), and NIDDK P30 DK078392 (Integrative Morphology and Gene Expression Cores). The funding sources did not play a role in the writing of the manuscript or the decision to submit it for publication, and did not play a role in data collection, analysis, interpretation; trial design; patient recruitment; or any aspect pertaining to the study.

Publisher Copyright:
© The Author(s) 2024.

All Science Journal Classification (ASJC) codes

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

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Braun, T., Feng, R., Amir, A., Levhar, N., Shacham, H., Mao, R., Toren, I., Abu-Saad, K., Zhuo, S., Efroni, G., Malik, A., Picard, O., Yavzori, M., Agranovich, B., Liu, T. C., Stappenbeck, T. S., Denson, L., Kalter-Leibovici, O., Gottlieb, E., ... Haberman, Y. (2024). Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. Nature Communications, 15(1), Article 3764. https://doi.org/10.1038/s41467-024-48106-6

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

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.",

author = "Tzipi Braun and Rui Feng and Amnon Amir and Nina Levhar and Hila Shacham and Ren Mao and Itamar Toren and Kathleen Abu-Saad and Shuoyu Zhuo and Gilat Efroni and Alona Malik and Orit Picard and Miri Yavzori and Bella Agranovich and Liu, {Ta Chiang} and Stappenbeck, {Thaddeus S.} and Lee Denson and Ofra Kalter-Leibovici and Eyal Gottlieb and Elhanan Borenstein and Eran Elinav and Minhu Chen and Shomron Ben-Horin and Yael Haberman",

note = "We thank all study participants. Support for the SOURCE study was provided by the Helmsley Charitable Trust (E.E., S.B.H., Y.H.). Other support included the ERC starting grant (Y.H., grant No. 758313), Tel Aviv University{\textquoteright}s Colton Center for Autoimmune Diseases (E.B., Y.H.), the Israel Science Foundation (Y.H., grant No. 785/22), the I-CORE program (Y.H., grants No. 41/11), Israel Science, Culture, and Sport (Y.H., grant no. 4361), and NIDDK P30 DK078392 (Integrative Morphology and Gene Expression Cores). The funding sources did not play a role in the writing of the manuscript or the decision to submit it for publication, and did not play a role in data collection, analysis, interpretation; trial design; patient recruitment; or any aspect pertaining to the study. Publisher Copyright: {\textcopyright} The Author(s) 2024.",

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doi = "10.1038/s41467-024-48106-6",

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Braun, T, Feng, R, Amir, A, Levhar, N, Shacham, H, Mao, R, Toren, I, Abu-Saad, K, Zhuo, S, Efroni, G, Malik, A, Picard, O, Yavzori, M, Agranovich, B, Liu, TC, Stappenbeck, TS, Denson, L, Kalter-Leibovici, O, Gottlieb, E, Borenstein, E, Elinav, E, Chen, M, Ben-Horin, S & Haberman, Y 2024, 'Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort', Nature Communications, vol. 15, no. 1, 3764. https://doi.org/10.1038/s41467-024-48106-6

TY - JOUR

T1 - Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort

AU - Braun, Tzipi

AU - Feng, Rui

AU - Amir, Amnon

AU - Levhar, Nina

AU - Shacham, Hila

AU - Mao, Ren

AU - Toren, Itamar

AU - Abu-Saad, Kathleen

AU - Zhuo, Shuoyu

AU - Efroni, Gilat

AU - Malik, Alona

AU - Picard, Orit

AU - Yavzori, Miri

AU - Agranovich, Bella

AU - Liu, Ta Chiang

AU - Stappenbeck, Thaddeus S.

AU - Denson, Lee

AU - Kalter-Leibovici, Ofra

AU - Gottlieb, Eyal

AU - Borenstein, Elhanan

AU - Elinav, Eran

AU - Chen, Minhu

AU - Ben-Horin, Shomron

AU - Haberman, Yael

N1 - We thank all study participants. Support for the SOURCE study was provided by the Helmsley Charitable Trust (E.E., S.B.H., Y.H.). Other support included the ERC starting grant (Y.H., grant No. 758313), Tel Aviv University’s Colton Center for Autoimmune Diseases (E.B., Y.H.), the Israel Science Foundation (Y.H., grant No. 785/22), the I-CORE program (Y.H., grants No. 41/11), Israel Science, Culture, and Sport (Y.H., grant no. 4361), and NIDDK P30 DK078392 (Integrative Morphology and Gene Expression Cores). The funding sources did not play a role in the writing of the manuscript or the decision to submit it for publication, and did not play a role in data collection, analysis, interpretation; trial design; patient recruitment; or any aspect pertaining to the study. Publisher Copyright: © The Author(s) 2024.

PY - 2024/5/4

Y1 - 2024/5/4

N2 - 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.

AB - 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.

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DO - 10.1038/s41467-024-48106-6

M3 - Article

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SN - 2041-1723

VL - 15

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 3764

ER -

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

Abstract

Bibliographical note

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