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New key publication: Environment dominates over host genetics in shaping human gut microbiota

08 March 2018

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.


  • 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
  • Eran Segal

Nature, 555(7695), 210–215.

Last modified:10 March 2018 10.24 p.m.

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