If you are sure and certain that you have bacteria in your digestive system, I would recommend a good probiotic.
Lactic bacteria produces lactase and natural Antibiotics that would help eliminate harmful and pathogenic bacteria in the GI tract.
A really good probiotic should contain live bacteria so that the bacteria count (reveival rate) is certain. It should be multi-strained so that the different bacteria get to work in the different regions of the GI tract. They would have to be colonizing to prevent re-infection or recurrence of the problem. Lastly, the bacteria needs to be protected against the strong stomach acids (pH 1-2) so that it can get to the intestines to work effectively.