In fairness, I should disclose that I do work for Starbucks….
I thought it was time that I look at coffee. Typical alternative medicine recommendation are no coffee, lots of yogurt containing Lactobacillus Acidophilus. I know that the latter is wrong advice for CFS/IBS. What about the former — coffee?
- “The results showed a direct association between the intake of red wine, a source of stilbenes, and the relative abundance of Bacteroides, and between the intake of coffee, rich in phenolic acids, and the abundance of Clostridium, Lactococcus and Lactobacillus genera.” 
- “Although unequivocal epidemiologic evidence indicates that the risk of Parkinson’s Disease is lower in smokers and coffee drinkers, explanations for these findings remain controversial[134,135]…. 30% lower among coffee drinkers than among non-drinkers…. Both cigarette and coffee consumption can alter the composition of the gut microbiota in a way that mitigates intestinal inflammation. …It has been also shown that consumption of coffee in both mice and humans induces a significant increase in the number of Bifidobacteria, which exert anti-inflammatory properties” 
- “Coffee is a relatively rich source of chlorogenic acids (CGA),…Similarly, an equivalent quantity of CGA (80·8 mg, matched with that in high-CGA coffee) induced a significant increase in the growth of Bifidobacterium spp. (P<0·05). CGA alone also induced a significant increase in the growth of the Clostridium coccoides-Eubacterium rectale group (P<0·05). 
- “Coffee consumption attenuated the increase in Firmicutes (F)-to-Bacteroidetes (B) ratio and Clostridium Cluster XI normally associated with high-fat feeding but also resulted in augmented levels of Enterobacteria.”
- “Our results show that the consumption of the coffee preparation resulting from water co-extraction of green and roasted coffee beans produce an increase in the metabolic activity and/or numbers of the Bifidobacterium spp. population, a bacterial group of reputed beneficial effects, without major impact on the dominant microbiota.”
- On the negative side: “In some studies restriction in consumption of fermented carbohydrates [usually Lactobacillus species], coffee and alcohol, as well as diet with elimination IgG-sensed food was also shown to be effective in irritable bowel syndrome.” 
If you have CFS, coffee may be good for your microbiome!