@Brett L My best guess is that the doctor wants to rule out (or identify) any GI infection before starting antibiotics. This is particularly important for C diff (which would make both Cipro and Flagyl a terrible idea for different reasons), but other GI infections could seem like pouchitis but need different treatments. So there’s no reliable test that can tell the doctor whether Cipro or Flagyl will be helpful for pouchitis, but there are certainly tests worth running before starting antibiotics.