Liz,
I was just speculating that it might be something "like" SIBO (Small Intestine Bacterial Overgrowth) since I am not emptying as often as other J-pouchers who do not have pouchitis/ulcers. And the small intestine normally doesn't have that much stool resting in it, but I'm speculating that mine is sitting there for a long time because I empty so infrequently.
en.wikipedia.org/wiki/Small_intestinal_bacterial_overgrowthSmall intestinal bacterial overgrowth (SIBO), is a disorder of excessive bacterial growth in the small intestine. Unlike the colon (or large bowel), which is rich with bacteria, the small bowel usually has fewer than 104 organisms per millilitre. Patients with bacterial overgrowth typically develop symptoms including nausea, bloating, vomiting, diarrhea, malnutrition, weight loss and malabsorption which is caused by a number of mechanisms.
My GI dismissed the idea pretty quickly so I didn't probe any further during my last visit; maybe I'll ask for the SIBO test next time. I recently cut out all sugars from my diet and I'm feeling much better and my gut is less noisy but I started the Augmentin at the same time. I also get Thrush really quickly when I start Flagyl, so I need to treat it constantly now. So maybe I do have a bacteria issue going on.
I have also taken Xifaxan for a few months and it didn't help that much.