Yes, we've done several CDSA, including those that do PCR study of the stool to also see dead stuff (e.g. anaerobic bacteria). We've also done many microbial urine organic tests to look for the byproduct from gut flora and see if there are any abnomalities. Also checked blood for immune reactions to normal flora, as well as IgG food panels to look for immune reactions to common foods. Yes, there was a huge bacterial overgrowth, about 20 times more than the maximum normal, per organic acids. Criptosporidium and rhodotorula have shown up in stool, as well as very large amounts of klebsiella. IgG reactions to over 50 foods (for a total of 200 tested). Intense immune reaction to saccharomyces, family of yeast used in breads, beer, kefir, etc... Pancreatic function seems impaired. Lots of maldigestion, very acidic stool pH. Low motility, impactions confirmed with x-rays, stools rarely formed, usually runny and light colored. Celiac panel negative.
He is taking about 200 billions CFUs total a day of four probiotic formulations he does very well with (Threelac, Culturelle, Reuteri and Super proBio). He also takes enzymes with meals, over-the-counter ones and prescription ones (Creon, pancreatic). We did try secretin nasal spray for a while with meals, to stimulate the pancreas, but did not see much. He is on a diet free of gluten and dairy and all the IgG reactive foods, all natural organic cooked from scratch and mostly pureed to make it more digestible. And of course, we have treated repetitively all the infections with whatever necessary, antibiotics, antifungals, antiparasite, and herbs.
After almost four years of that it has helped immensely, but the gut is not 'healed'. It is just kept in better shape through heavy support. But something is attacking it, maybe XMRV directly, or just autoimmune. I still totally agree that working on the gut is worth it. It does need to be addressed from many sides simulatenously, and there is a lot of trial and error. Elimination diets have been the most effective weapon for us.
I do have Gastrocrom sitting on my counter and need to try this. It blocs the mast cells during meals to prevent food reactions. I am also going to try another mast cell blocker. He is already on singulair (for its non-steroid anti-inflamation properties), which is already supposed to help some with the GI tract as well.