Alternative protein sources to soybean meal (SBM), such as Cottonseed Meal (CSM) and Corn Distillers Dried Grains with Solubles (DDGS) can have lower quality protein levels and reduced digestibility. Supplementing protease helps monogastrics that lack adequate levels of endogenous enzymes to digest proteins in the diet, which reduces the flow of undigested protein and other anti-nutritionals entering the large intestine. This indigestible protein serves as a fermentation substrate for undesirable bacterial strains, such as Escherichia coli, Clostridium perfringens, Salmonella and Campylobacter in the gut. The proteins will be used by these harmful bacteria as nutrients. These pathogenic bacteria can then increase in population, shifting the balance of intestinal microflora against beneficial strains.