Background: Vitamin D /Vitamin D receptor (VDR) involve environmental factors, host factors, and microbiome. Vdr gene variation shapes the human microbiome, and Vitamin D / VDR deficiency leads to dysbiosis and is associated with various diseases, including cancer, infection, and inflammatory bowel disease. To date, research on Vitamin D /VDR deficiency has focused upon bacteria and viruses. The impact of VDR deficiency on fungi and archaea is unknown. We hypothesize that VDR deficiency alters the archaeome and mycobiome, thus altering the metabolites in a tissue-specific manner.
Methods: To test our hypothesis, we conditionally deleted the VDR in Paneth cells (VDR^ΔPC), intestinal epithelial cells (VDR^ΔIEC), or myeloid cells (VDR^ΔLyz) in mice and collected feces for shotgun metagenomic sequencing and untargeted metabolomics. We also tested sex-subsets to investigate the sex-dependent action of VDR deficiency. Finally, functional metagenomic analyses and metabolite measurement provided more evidence of the impact of microbial perturbations v.s. the VDR status in different tissues.
Results: We found that fungi were significantly altered in each knockout (KO) group, compared to the VDR^Loxp control group. The VDR^ΔLyz mice had the most altered fungi species (3 depleted and 7 enriched), then the VDR^ΔPC mice (6 depleted and 2 enriched), and the VDR^ΔIEC mice (1 depleted and 1 enriched). The methanogen Methanofollis limitans was enriched in the VDR^ΔPC and VDR^ΔLyz mice and two archaea species (Thermococcus piezophilus and Sulfolobus acidocaldarius) were enriched in VDR^ΔPC mice, compared to VDR^Loxp mice. The genus Methanofollis and the species Methanofollis liminatans showed increased abundant in both sex-subsets of the VDR^ΔPC and VDR^ΔLyzgroups. Sulfolobus acidocaidarius was increased in the male VDR^ΔPC mice but not the female. Significant correlations existed among altered fungi, archaea, bacteria, and viruses in the specific-tissue VDR KO mice. Functional metagenomic analysis showed changes in several biologic functions. Most of these were decreased in the knockout group (Sulfate adenyltransferase subunits 1 and 2, Manganese transport protein, DNA repair protein recombination protein O, Serine recombinase, and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase), but 3 were increased (Adenosylcobinamide-phosphate synthase, Adenylcobyric acid synthase, and L-lactate dehydrogenase complex protein Lldf). Examination of fecal metabolites indicate the involvement of altered sulfate reduction associated with the VDR status.
Conclusions: VDR deficiency caused altered fungi and archaea in a tissue- and sex-dependent manner. These results provide a foundation about the impact of VDR deficiency on fungi and archaea. It opens the door for further studies to determine how mycobiome and cross-kingdom interactions in microbiome community contribute to risks of diseases.

Duncan Claypool

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