I just have seen my specialist for the pouch check up. He has prescribed me Metronidazole and Ciprofloxacin which I will of course take but I'm concerned about taking such strong antibiotics. I was told that it is not unusual to have pouchitis and if this is the case are such strong antibiotics the best way forward? Is it better to let my own immune system deal with it or is pouchitis really only treatable with antibiotics?
I think your doctor is right, Take the antibiotics. Take the whole prescription, even if you feel better and have fewer symptoms after a few days. If you don't, some bacteria will remain and come back even stronger the next time. By taking both Metronidazole and Ciprofloxacin you will cover it.