In my last post, one of the studies had a surprise — Vitamin D supplementation alters the microbiome. I have advocated Vitamin D based on observation studies published on PubMed for CFS — “it improves symptoms, the mechanism is a matter of speculation”
- “Compared with the other groups, untreated patients with multiple sclerosis had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation.” 
That lead me to do a more detail search on Pub Med.
- Vitamin D receptor pathway is required for probiotic protection in colitis.  “We found that the probiotics Lactobacillus rhamnosus strain GG (LGG) and Lactobacillus plantarum (LP) increased VDR protein expression in both mouse and human intestinal epithelial cells.”
- “Vitamin D3 supplementation changed the gut microbiome in the upper GI tract (gastric corpus, antrum, and duodenum). We found a decreased relative abundance of Gammaproteobacteria including Pseudomonas spp. and Escherichia/Shigella spp. and increased bacterial richness.” 
- Dysbiosis caused by vitamin D receptor deficiency confers colonization resistance to Citrobacter rodentium through modulation of innate lymphoid cells. 
- Vitamin D and prebiotics may benefit the intestinal microbacteria and improve glucose homeostasis in prediabetes and type 2 diabetes.
- “. Vitamin D is beneficial in inflammatory bowel diseases because it regulates multiple checkpoints and processes essential for homeostasis in the gut. Vitamin D inhibits IFN-γ and IL-17 production while inducing regulatory T cells. In addition, vitamin D regulates epithelial cell integrity, innate immune responses, and the composition of the gut microbiota.” 
- Gut microbiota, probiotics, and vitamin D: interrelated exposures influencing allergy, asthma, and obesity?  ” there is emerging evidence that the vitamin D pathway might be important in gut homeostasis and in signaling between the microbiota and the host.”
- ” a decreased dietary intake of vitamins including vitamin D (p<0.05) that correlated with differences in fecal microbiota composition but not fecal genotoxicity.” 
Sufficient vitamin D intake impacts microbiome (and been documented to reduce symptoms in CFS see this post). That is, it alters the microbiome in the right way! If you have VDR, then two probiotics are recommended because of that, Lactobacillus rhamnosus strain GG (LGG) and Lactobacillus plantarum (LP).
If you do not know if you have VDR but have done 23AndMe Dna analysis, there are several pages on the web that may help you to determine that.