On a recent group post I speculated that the high Vitamin 1,25D levels seen in CFS and other autoimmune diseases may be caused by specific bacteria in the microbiota. Hence, the appropriate antibiotics or probiotic to muscle them out (L. Reuteri, Mutaflor, Prescript Assist) may be the appropriate treatment.
Of course, when I speculate — I tend to follow it up with some searching of pubmed to see if there is evidence pro or contrary.
“Environment and genetic are both relevant in determining development of Multiple Sclerosis. Many epidemiological observations converge on indicating EBV infection and Vitamin D levels as major players among the environmental factors. Bacteria and bacterial products are however potent triggers of immune responses, and recent work from several laboratories indicates that the microbiota plays a prominent role in “priming” or protecting individuals for development of experimental autoimmune diseases.” 
“Current evidence supports a role for gut colonization in promoting and maintaining a balanced immune response in early life. An altered or less diverse gut microbiota composition has been associated with atopic diseases, obesity, or both. Moreover, certain gut microbial strains have been shown to inhibit or attenuate immune responses associated with chronic inflammation in experimental models. …. Finally, there is emerging evidence that the vitamin D pathway might be important in gut homeostasis and in signaling between the microbiota and the host. Given the complexity of the gut micriobiota, additional research is needed before we can confidently establish whether its manipulation in early life can prevent or treat asthma, obesity, or both.” 2011
“However, other dietary factors affect the microbiota in different ways. Distinguishing cause from effect, and characterizing the relative roles of human and microbial genes, diet, age of onset, gender, life style, smoking history, ethnic background, environmental exposures, and medications, will require innovative and internationally integrated approaches.” 2012
“The current review will discuss this by comparing the intracrine, paracrine and endocrine metabolic systems that influence the interaction between vitamin D and the immune system.” 2012
In short, Vitamin D and probiotics may be both needed. It may be a significant component in signaling (controlling production levels). There were no studies on microbiota and 1,25D. 🙁