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Antibiotics - in a lot of pain

I was in the hospital for what I thought was an obstruction. After the CT scan,  I was diagnosed with a partial obstruction and a diseased colon and pouchitis. I was given two antibiotics, Flagyl and Cipro. I take 500 mg of each twice a day. I have been in a lot of pain since I started eating. Has anyone else been on high doses antibiotics and suffered with a lot of pain and extremely watery diarrhea. I was wondering if maybe I didn't give my bowel enough time to rest prior to eating.  

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