I wouldn't suggest killing off your colon bacteria with antibiotics, as your good flora is much more sensitive than the bad stuff- and you may not kill it, but just weaken your own immune system in the process. Instead, try starving off colon bacteria by cutting back on the carbs and fiber for a while, which they feed on.
For something similar, I was put on an almost all liquid diet for 3 days- eating only chicken noodle soup, soda crackers, and lots of fluids to kill the bacteria. Then keep eating mildly but introduce a fiber supplement (about another 3 days). This will also help if you have had any changes in stool.
You can gradually reintroduce your regular diet, and like honeybunny said, you will be able to better guess your trigger foods. Elimination diet can be frustrating (because you get sick of things like chicken noodle really fast!) but also the most effective to find any intolerance (such as gluten, etc)
Good luck and good health!