Antibiotics wipe out bad and good bacteria, and cipro in particular seems to cause more problems after a course. It's wise to always follow up antibiotics with probiotics to reestablish some of the good bacteria for a happy, healthy balance! Your best course of action would be a probiotic supplement containing multiple strains, a prebiotic to provide fuel for the good bacteria to get an extra boost, and digestive enzymes (protease, amylase, and lipase) with meals if you need any relief from indigestion. These won't hurt you any. You may also be able to find additional advice by searching for more information about antibiotics/cipro causing a gut flora imbalance... you aren't alone in this!