Betaine HCl increases stomach acidity which break down meat fibers and other foods into a liquid mixture called chyme. When that chyme is acid enough, it triggers the release of bile from the gallbladder and the release of enzymes and bicarbonate (pancreas) to neutralize the acid. Using a supplement of enzymes would still be a good choice along with Betaine HCl, although I'm not sure if vegetarian enzymes or pancreatin is better.
This have a sterilizing action (the high acid and then the bile) on the small intestine.