SAFF, Flagyl does come as a rectal suppository in some countries. I see that you're in Australia, so it might be available to you without my wacky idea. Your doctor is partially correct, that the Flagyl is absorbed into the blood in either case. However, we don't really know how antibiotics help in pouchitis, we just make some reasonable guesses. A higher gut concentration of antibiotic may be very important to success.