I saw the new guidelines for microscopic colitis, and they say not to use any probiotics, perhaps because of a reaction to commensal bacteria like in Crohn’s. What’s your experience with this?

Chris Kresser:   I was just reading a paper not too long ago. I can’t remember if I’ve mentioned it to you guys, but it was a meta-analysis of FMT in patients with IBD, and what they found is that a full 25 percent of patients had an adverse reaction. If you think of one of the proposed etiologies of Crohn’s and IBD, in general, an inappropriate immune reaction to the body’s commensal microflora. In other words, the patient is attacking their own beneficial gut bacteria. And so if you do a procedure like an FMT that introduces a huge amount of beneficial bacteria, then you could see how that could potentially make someone much worse if that was the issue. And the reason perhaps that it only makes 25 percent of patients worse is that Crohn’s and IBD are multifactorial, as well. I’ve believed this for many, many years. I don’t think there’s a single cause or etiology for inflammatory bowel disease. I think there are probably multiple etiologies, and so that could explain why some patients get better with FMT who have IBD and some patients get worse, and it would explain why some patients with microscopic colitis and IBD get worse with probiotics and some get better. But not all probiotics are created equal, and there are some probiotics that have been shown to be more effective for IBD, which I think I mentioned in the gut treatment unit. We talked about Mutaflor, E. coli Nissle being one of the probiotics that can be really useful in IBD. So I don’t know that I would follow that recommendation and avoid them entirely, but I might experiment with more specific probiotics that have been shown to be helpful in inflammatory bowel disease.