Environment dominates over host genetics in shaping human gut microbiota

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 Vich Vila, Niv Zmora, Meirav Pevsner-Fischer, David Israeli, Noa Kosower, Gal Malka, Bat Chen Wolf, Tali Avnit-Sagi, Maya Lotan-Pompan, Adina Weinberger, Zamir Halpern, Shai Carmi, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Elinav () and Eran Segal ()
Additional contact information
Daphna Rothschild: Weizmann Institute of Science
Omer Weissbrod: Weizmann Institute of Science
Elad Barkan: Weizmann Institute of Science
Alexander Kurilshikov: University of Groningen, University Medical Center Groningen
Tal Korem: Weizmann Institute of Science
David Zeevi: Weizmann Institute of Science
Paul I. Costea: Weizmann Institute of Science
Anastasia Godneva: Weizmann Institute of Science
Iris N. Kalka: Weizmann Institute of Science
Noam Bar: Weizmann Institute of Science
Smadar Shilo: Weizmann Institute of Science
Dar Lador: Weizmann Institute of Science
Arnau Vich Vila: University of Groningen, University Medical Center Groningen
Niv Zmora: Weizmann Institute of Science
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
Gal Malka: Weizmann Institute of Science
Bat Chen Wolf: Weizmann Institute of Science
Tali Avnit-Sagi: Weizmann Institute of Science
Maya Lotan-Pompan: Weizmann Institute of Science
Adina Weinberger: 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
Shai Carmi: Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem
Jingyuan Fu: University of Groningen, University Medical Center Groningen
Cisca Wijmenga: University of Groningen, University Medical Center Groningen
Alexandra Zhernakova: University of Groningen, University Medical Center Groningen
Eran Elinav: Weizmann Institute of Science
Eran Segal: Weizmann Institute of Science

Nature, 2018, vol. 555, issue 7695, 210-215

Abstract: 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.

Date: 2018
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DOI: 10.1038/nature25973

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