Could be allergic to some of the foods you are eating... a food allergy test would be good
- change carb sources to Amaranth, Millet, Wild Rice, or Quinoa... and don't use too much fat with carb meals perhaps.
- use high quality protein shakes/meat/foods... and switch up the meats daily.
- apple cider vinegar is good like Eric said
- enzymes and pro biotics, and do a cleans/fast( probably would do this first)