I worked on the development of Cipro. This quinolone antibiotic is not effective against anaerobic bacteria, those bacteria that live without oxygen. Our intestines are anaerobic and hence filled with these bacteria. The Cipro would not likey have a huge effect on this population of bacteria, particularly if you were on Cipro for a short time. Perhaps you had some disturbances in gut microflora from other antibiotics you were on at the time. Generally, even when this population is disturbed it eventually goes back to normal after stopping the drug.
Even without ever taking an antibiotic, excess carb consumption will result in large amounts of intestinal gas. Some people can handle this excess gas, some people, like those suffering from GERD and IBS cant and problems ensue. Cutting carbs will dramatically improve this situation. If you serious and you get some guidance on this approach, you should be able (with consultation by your doc) to stop the meds in a couple of days. Some people taper off the PPIs over a week or two, some just stop.
Good luck. I think you should try it.