I'm going through a similar situation, but my bacteria overgrowth was in the large intestines. If you have true SIBO (the bacteria is in the small intestines), my understanding from my GI doctors is that you don't want probiotics until your body's flushing capability is working since you shouldn't have any bacteria (good or bad) in the small intestines. For me, it turns out it was in the large intestines, so probiotics are fine. But I had the same dilemma about trying to feed good bacteria while not feeding the bad bacteria. I got rid of most of my overgrowth with elemental diets (the retail version is Vivonex, but you can make homemade versions), and then when the bad bacteria was low I started introducing heavy good probiotics. Look at Prescript-assist as it's soil based and better for those of us with issues with dairy based strands. But again, if your issue is that bacteria is staying inside the small intestines due to non-flushing, then be careful about any probiotics till that's working again.