What material found in the digestive system aids digestion and also kills pathogens

Hydrochloric acid is secreted in the stomach for digestion.

There are two things that follow this descriptions. Biotic flora or bacteria found in the gut does help with digestion of objects that we would normally have a harder time breaking down. Additionally these probiotics are what we consider good bacteria and many of which actually also kill bad bacteria and certain pathogens.

Additionally the main components of actual digestion that we excrete including Saliva, Hydrochloric Acid, and Bile all aid in digestion (bile primarily is good with breaking down oils) and all are capable of destroying certain pathogens.

Blood transfusions were rarely done and often fatal; they were outlawed until the nineteenth century.