IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v555y2018i7695d10.1038_nature25973.html
   My bibliography  Save this article

Environment dominates over host genetics in shaping human gut microbiota

Author

Listed:
  • Daphna Rothschild

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Omer Weissbrod

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Elad Barkan

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Alexander Kurilshikov

    (University of Groningen, University Medical Center Groningen)

  • Tal Korem

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • David Zeevi

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Paul I. Costea

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Anastasia Godneva

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Iris N. Kalka

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Noam Bar

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Smadar Shilo

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Dar Lador

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Arnau Vich Vila

    (University of Groningen, University Medical Center Groningen
    University of Groningen, University Medical Center Groningen)

  • Niv Zmora

    (Weizmann Institute of Science
    Tel Aviv Sourasky Medical Center
    Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University)

  • Meirav Pevsner-Fischer

    (Weizmann Institute of Science)

  • David Israeli

    (Day Care Unit and the Laboratory of Imaging and Brain Stimulation, Kfar Shaul Hospital, Jerusalem Center for Mental Health)

  • Noa Kosower

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Gal Malka

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Bat Chen Wolf

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Tali Avnit-Sagi

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Maya Lotan-Pompan

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Adina Weinberger

    (Weizmann Institute of Science
    Weizmann Institute of Science)

  • Zamir Halpern

    (Research Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University
    Digestive Center, Tel Aviv Sourasky Medical Center)

  • Shai Carmi

    (Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem)

  • Jingyuan Fu

    (University of Groningen, University Medical Center Groningen
    University of Groningen, University Medical Center Groningen)

  • Cisca Wijmenga

    (University of Groningen, University Medical Center Groningen
    K.G. Jebsen Coeliac Disease Research Centre, University of Oslo)

  • Alexandra Zhernakova

    (University of Groningen, University Medical Center Groningen)

  • Eran Elinav

    (Weizmann Institute of Science)

  • Eran Segal

    (Weizmann Institute of Science
    Weizmann Institute of Science)

Abstract

Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.

Suggested Citation

  • Daphna Rothschild & Omer Weissbrod & Elad Barkan & Alexander Kurilshikov & Tal Korem & David Zeevi & Paul I. Costea & Anastasia Godneva & Iris N. Kalka & Noam Bar & Smadar Shilo & Dar Lador & Arnau Vi, 2018. "Environment dominates over host genetics in shaping human gut microbiota," Nature, Nature, vol. 555(7695), pages 210-215, March.
  • Handle: RePEc:nat:nature:v:555:y:2018:i:7695:d:10.1038_nature25973
    DOI: 10.1038/nature25973
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature25973
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1038/nature25973?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Zahraa Al Bander & Marloes Dekker Nitert & Aya Mousa & Negar Naderpoor, 2020. "The Gut Microbiota and Inflammation: An Overview," IJERPH, MDPI, vol. 17(20), pages 1-21, October.
    2. Qiwen Cheng & Rosa Krajmalnik-Brown & John K. DiBaise & Juan Maldonado & M. Aaron Guest & Michael Todd & Shelby L. Langer, 2023. "Relationship Functioning and Gut Microbiota Composition among Older Adult Couples," IJERPH, MDPI, vol. 20(8), pages 1-17, April.
    3. Karolina Skonieczna-Żydecka & Ewa Stachowska & Dominika Maciejewska & Karina Ryterska & Joanna Palma & Maja Czerwińska-Rogowska & Mariusz Kaczmarczyk & Anna Gudan & Honorata Mruk & Barbara Świniarska , 2018. "The Digestive Health among Participants of the Woodstock Rock Festival in Poland—A Cross-Sectional Survey," IJERPH, MDPI, vol. 15(10), pages 1-13, October.
    4. Zhirui Cao & Dejun Fan & Yang Sun & Ziyu Huang & Yue Li & Runping Su & Feng Zhang & Qing Li & Hongju Yang & Fen Zhang & Yinglei Miao & Ping Lan & Xiaojian Wu & Tao Zuo, 2024. "The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    5. Jos A. Bosch & Max Nieuwdorp & Aeilko H. Zwinderman & Mélanie Deschasaux & Djawad Radjabzadeh & Robert Kraaij & Mark Davids & Susanne R. Rooij & Anja Lok, 2022. "The gut microbiota and depressive symptoms across ethnic groups," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Andrea Quagliariello & Alessandra Modi & Gabriel Innocenti & Valentina Zaro & Cecilia Conati Barbaro & Annamaria Ronchitelli & Francesco Boschin & Claudio Cavazzuti & Elena Dellù & Francesca Radina & , 2022. "Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    8. Ren Dodge & Eric W. Jones & Haolong Zhu & Benjamin Obadia & Daniel J. Martinez & Chenhui Wang & Andrés Aranda-Díaz & Kevin Aumiller & Zhexian Liu & Marco Voltolini & Eoin L. Brodie & Kerwyn Casey Huan, 2023. "A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    9. Jun Ueyama & Mai Hayashi & Masaaki Hirayama & Hiroshi Nishiwaki & Mikako Ito & Isao Saito & Yoshio Tsuboi & Tomohiko Isobe & Kinji Ohno, 2022. "Effects of Pesticide Intake on Gut Microbiota and Metabolites in Healthy Adults," IJERPH, MDPI, vol. 20(1), pages 1-13, December.
    10. C. E. Dubé & M. Ziegler & A. Mercière & E. Boissin & S. Planes & C. A. -F. Bourmaud & C. R. Voolstra, 2021. "Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    11. Ke Tao & Ib T. Jensen & Sha Zhang & Eber Villa-Rodríguez & Zuzana Blahovska & Camilla Lind Salomonsen & Anna Martyn & Þuríður Nótt Björgvinsdóttir & Simon Kelly & Luc Janss & Marianne Glasius & Rasmus, 2024. "Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Yee Sang Wong & Nicholas John Osborne, 2022. "Biodiversity Effects on Human Mental Health via Microbiota Alterations," IJERPH, MDPI, vol. 19(19), pages 1-13, September.
    13. Qinnan Yang & Mallory Haute & Nate Korth & Scott E. Sattler & John Toy & Devin J. Rose & James C. Schnable & Andrew K. Benson, 2022. "Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    14. Fanette Fontaine & Sondra Turjeman & Karel Callens & Omry Koren, 2023. "The intersection of undernutrition, microbiome, and child development in the first years of life," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    15. Kerstin Thriene & Karin B. Michels, 2023. "Human Gut Microbiota Plasticity throughout the Life Course," IJERPH, MDPI, vol. 20(2), pages 1-14, January.
    16. Lharbi Dridi & Fernando Altamura & Emmanuel Gonzalez & Olivia Lui & Ryszard Kubinski & Reilly Pidgeon & Adrian Montagut & Jasmine Chong & Jianguo Xia & Corinne F. Maurice & Bastien Castagner, 2023. "Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    17. Manish Boolchandani & Kevin S. Blake & Drake H. Tilley & Miguel M. Cabada & Drew J. Schwartz & Sanket Patel & Maria Luisa Morales & Rina Meza & Giselle Soto & Sandra D. Isidean & Chad K. Porter & Mark, 2022. "Impact of international travel and diarrhea on gut microbiome and resistome dynamics," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    18. Braden T Tierney & Yingxuan Tan & Zhen Yang & Bing Shui & Michaela J Walker & Benjamin M Kent & Aleksandar D Kostic & Chirag J Patel, 2022. "Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research," PLOS Biology, Public Library of Science, vol. 20(3), pages 1-18, March.
    19. Carsten Eriksen & Janne Marie Moll & Pernille Neve Myers & Ana Rosa Almeida Pinto & Niels Banhos Danneskiold-Samsøe & Rasmus Ibsen Dehli & Lisbeth Buus Rosholm & Marlene Danner Dalgaard & John Penders, 2023. "IgG and IgM cooperate in coating of intestinal bacteria in IgA deficiency," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:555:y:2018:i:7695:d:10.1038_nature25973. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.