Vitamin D and the gut microbiome: a systematic review of in vivo studies

  • Mary Waterhouse
  • Bronwyn Hope
  • Lutz Krause
  • Mark Morrison
  • Melinda M. Protani
  • Martha Zakrzewski
  • Rachel E. NealeEmail author
Original Contribution



Variation in the human microbiome has been linked with a variety of physiological functions, including immune regulation and metabolism and biosynthesis of vitamins, hormones, and neurotransmitters. Evidence for extraskeletal effects of vitamin D has been accruing and it has been suggested that the effect of vitamin D on health is partially mediated through the microbiome. We aimed to critically evaluate the evidence linking vitamin D and the gastrointestinal microbiome.


We systematically searched the Embase, Web of Science, PubMed and CINAHL databases, including peer-reviewed publications that reported an association between a measure of vitamin D and the gastrointestinal microbiome in humans or experimental animals.


We included 10 mouse and 14 human studies. Mouse studies compared mice fed diets containing different levels of vitamin D (usually high versus low), or vitamin D receptor knockout or Cyp27B1 knockout with wild-type mice. Five mouse studies reported an increase in Bacteroidetes (or taxa within that phylum) in the low vitamin D diet or gene knockout group. Human studies were predominantly observational; all but two of the included studies found some association between vitamin D and the gut microbiome, but the nature of differences observed varied across studies.


Despite substantial heterogeneity, we found evidence to support the hypothesis that vitamin D influences the composition of the gastrointestinal microbiome. However, the research is limited, having been conducted either in mice or in mostly small, selected human populations. Future research in larger population-based studies is needed to fully understand the extent to which vitamin D modulates the microbiome.


Gut microbiota Microbiome Vitamin D Systematic review 



RE Neale is funded by a fellowship from the National Health and Medical Research Council of Australia.

Author contributions

BH and REN conceived the study. BH, REN, and MW identified citations for inclusion and extracted relevant information. LK, MM, MMP and MZ provided critical comment on the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

394_2018_1842_MOESM1_ESM.pdf (222 kb)
Supplementary material 1 (PDF 221 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Mary Waterhouse
    • 1
  • Bronwyn Hope
    • 1
  • Lutz Krause
    • 2
  • Mark Morrison
    • 2
  • Melinda M. Protani
    • 3
  • Martha Zakrzewski
    • 1
  • Rachel E. Neale
    • 1
    Email author
  1. 1.Population Health DepartmentQIMR Berghofer Medical Research InstituteBrisbaneAustralia
  2. 2.Faculty of MedicineThe University of Queensland Diamantina Institute, Translational Research InstitituteBrisbaneAustralia
  3. 3.School of Public HealthThe University of QueenslandBrisbaneAustralia

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