Enzymes are in your foods. These enzymes help your body digest properly.
Now, if enzymes in food worked all by themselves every plant would be mush already. Enzymes work in conjuction with your digestive system.
A lack of acid in the stomach, leading to a problem with digesting food can turn into a problem in the lower bowels as well. If you have a lack of acid in your stomach, please look up information about H.pylori which could be effecting your system.
You could also look into the lower bowel balance formulas, like Dr. Christopher's. I know that MH has some.