I tried using VSL #3 probiotics and they ended up making me much worse off...probiotics work differently for everybody, it seems. Be careful with those. It is possible to use probiotics in conjunction with antibiotics, contrary to what one would assume, but it doesn't need to be a very powerful probiotic.
I'm currently trying to build a list of antibiotics that people have used to treat their pouchitis flare ups, and so far I have:
1. Tetracycline (no longer available, worldwide shortage)
2. Cipro (really strong but okay for longer term usage)
3. Flagyl (super strong but can have some side effects like you describe, and not healthy for long-term usage)
4. Xifaxin (which can be fairly expensive, up to $350 a bottle uninsured, but it is very effective from what I hear)
5. Amoxicillin (Augmentin) (this is the best lower-powered AB I've used since Tetracycline, very effective for my own needs, have you tried it for maintenance?)
6. Keflex (this can work, while it did work for me by fixing the pouchitis infection, it produced a cuffitis reaction that made life miserable, so be careful there)
Here's a neat article talking about some other possibilities (including budesonide enemas and immunosuppressants):
How Do You Treat Pouchitis?There are a lot of combinations that can go on, including steroids, but nobody wants that. My own doctor put it in this order: Probiotics, Antibiotics, Steroids, Surgery. I see steroids as a cliff I don't want to even approach, much less jump off, but if I have to, so be it.
Everybody here in the forum is so helpful, I'm sure you'll continue to find more suggestions as time goes on. Hang in there!