Although this has fallen off the map a bit in light of XMRV's attention, I still think gut ecology is more important than ever. Doc often talks about the gut and brain recovery going hand in hand, especially with the gut being scientifically discussed as the second brain and also housing 70% of the immune system.
With that said, I think it's important not to take probiotics willy-nilly. D-lactate needs to be avoided. Cheney on De Meirleir's findings
"The bottom line is that they showed increased bacterial overgrowth in the GI tract in CFS that produces bacterial derived D-Lactate that is likely responsible for significant cognitive problems, especially memory. There is also a high likelihood of increased H2S associated with this D-Lactate which will cause even more weakness and fatigue and put you in bed as well as disrupt sleep." - http://www.cheneyclinic.com/gut-dysbiosis-modulates-significant-cfs-symptoms/247
Kefir was recommended by many at first, but I can't tolerate any type of dairy--even goat milk. Some CFS patients don't seem to have this problem, but I sneer at thee Asian gene. I tried a coconut kefir from Whole Foods, but they add lactic acid and a bunch of fillers (guar gum etc) to it. Both tested really poorly for me. Also, the Sanpharma protocol didn't heal my gut completely. It seemed improved until I tried experimenting with kefir, and the last few days it's been in full rebellion mode.
In my search for a d-lactate free probiotic, I found this great summary by CFS Patient Advocate:
VSL #3 is seen as a quite good and well-researched probiotic. It is ordered on the internet. Culturelle, available in grocery stores and pharmacies, is also well researched, and has the advantage of being D-Lactate free. D-Lactate producing Lactobacillus and Bifidobacter probiotics are seen as a problem for CFS patients. Custom Probioticsmakes a D-Lactate free combination of Lacto and Bifido. Harry, who runs Custom Probiotics, seems happy to talk about the advantages of his products, which he has designed himself. Mutaflor makes a probiotic that is seen as providing great benefit. This product can be purchased in Germany and shipped to America. De Meirleir and Cheney both use this product. Recently, Dr. Alan Logan on Cort Johnson’s most valuable site, has been promoting Align, a bifidobacterial probiotic. Align has a small amount of sugar in it, and is also D-Lactate free. Dr. Guyer recommends Allergy Research’s Russian Immune for boosting the immune system.
There is continuing research into various probiotics and their relationship to particular illnesses and to health in general. For instance. there is a probiotic in development that supposedly eats oxalates, for those of you that have that particular problem.
So it would be prudent to keep reading about probiotic research and keep in mind that it might also be useful to rotate probiotics.
I just purchased Custom Probiotics http://www.customprobiotics.com/custom-probiotics-d-lactate.htm . I have no financial affiliation with this or any other company listed above. Will update on how it goes. The only other probiotic I'm taking now is Florastor, but Culturelle (listed above) has tested well for me in the past.