Science news has a recent article entitled “Microbiome Changed by Gluten Increases Incidences of Type 1 Diabetes“, since gluten sensitivities is common with CFS and there are similarities to Type-3 diabetes, I thought that I should drill down on this via PubMed.
First, it looks like there may be a probiotic to help in the works . For celiac disease, we appear to have lower Lactobacillus and Bifidobacterium species/ volume  — which suggests that Lactobacillus Reuteri and Align (Bifidobacterium infantis 35624) has the potential to be helpful. Another 2013 studies suggests that high Bacteroidetes (phyla) and Parabacteriodes (genus) may be a factor. The likely missing bacteria are Rothia bacteria according to this  study (there is already a patent filed on such use), however there appear to be no commercially available probiotics.
I also found a most interesting article indicating the the pH of drinking water impacts gut bacteria — yes drinking water! [5 Nov 2013] This has implication on what you drink — soda pop pH may be a factor for diabetes (beyond the usual sugar issue). There is a chart of pH for some foods here. You may wish to shift the food and drink you consume to higher pH (less acid values). There are various sites that will give lists of acid and alkaline foods – WARNING: sites may disagree – for example one site says orange juice is low ph (acid) and another site say it is alkaline.
The safest approach may be adding ½ a teaspoon of baking soda to a gallon of water. Also, we are not talking about alkalizing blood (which is often an alternative medicine approach), but about drinking alkalize water to alter gut bacteria. Often the alkalizing blood techniques does do by acidifying the stomach (exact opposite of this intent).