Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota

Nat Genet. 2016 Nov;48(11):1396-1406. doi: 10.1038/ng.3695. Epub 2016 Oct 10.

Abstract

Human gut microbiota is an important determinant for health and disease, and recent studies emphasize the numerous factors shaping its diversity. Here we performed a genome-wide association study (GWAS) of the gut microbiota using two cohorts from northern Germany totaling 1,812 individuals. Comprehensively controlling for diet and non-genetic parameters, we identify genome-wide significant associations for overall microbial variation and individual taxa at multiple genetic loci, including the VDR gene (encoding vitamin D receptor). We observe significant shifts in the microbiota of Vdr-/- mice relative to control mice and correlations between the microbiota and serum measurements of selected bile and fatty acids in humans, including known ligands and downstream metabolites of VDR. Genome-wide significant (P < 5 × 10-8) associations at multiple additional loci identify other important points of host-microbe intersection, notably several disease susceptibility genes and sterol metabolism pathway components. Non-genetic and genetic factors each account for approximately 10% of the variation in gut microbiota, whereby individual effects are relatively small.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Animals
  • Bacteria / classification
  • Bacteria / genetics
  • Cohort Studies
  • Diet
  • Female
  • Gastrointestinal Microbiome*
  • Genome-Wide Association Study
  • Humans
  • Male
  • Mice
  • Mice, Knockout
  • Middle Aged
  • Polymorphism, Single Nucleotide
  • Receptors, Calcitriol / genetics*

Substances

  • Receptors, Calcitriol
  • VDR protein, human