The gut is a very complex system and there could be a number of factors involved. The best thing to do is get proper testing and not make presumptions on what pathogen (if it is a pathogen related issue) you have. It could be a simple issue of having low amounts of probiotics, in which case make sure you adequate fiber so the probiotics can multiply.
The best testing is thru Metametrix GI Effects Stool test (use panel #2105).