Hi..., Protein is primarily broken down by hydrochloric acid in the stomach and pancreatic protein enzymes in the upper small intestine,.... Failure to effectively digest protein in the upper gastrointestinal tract allows larger undigested proteins to pass into the bowel where it is often decomposed by bacterial putrification – a process that can lead to diarrhoea, cramps, flatulence, bloating and other digestive complaints... Consult Physician....