Digestion
Digestion begins in the mouth with the secretion of saliva and its digestive enzymes. Food is formed into a bolus by the mechanical mastication and swallowed into the esophagus from where it enters the stomach through the action of peristalsis. Gastric juice contains hydrochloric acid and pepsin which would damage the walls of the stomach and mucus is secreted for protection. In the stomach further release of enzymes break down the food further and this is combined with the churning action of the stomach. The partially digested food enters the duodenum as a thick semi-liquid chyme. In the small intestine, the larger part of digestion takes place and this is helped by the secretions of bile, pancreatic juice and intestinal juice. The intestinal walls are lined with villi, and their epithelial cells is covered with numerous microvilli to improve the absorption of nutrients by increasing the surface area of the intestine.
Assimilation (biology)
Most foods are composed of largely indigestible components depending on the enzymes and effectiveness of an animal's digestive tract. The most well-known of these indigestible compounds is cellulose; the basic chemical polymer in the makeup of plant cell walls. Most animals, however, do not produce cellulase; the enzyme needed to digest cellulose. However some animal and species have developed symbiotic relationships with cellulose-producing bacteria (see termites and metamonads.) This allows termites to use the energy-dense cellulose carbohydrate. Other such enzymes are known to significantly improve bio-assimilation of nutrients. Because of the use of bacterial derivatives, enzymatic dietary supplements now contain such enzymes as amylase, glucoamylase, protease, invertase, peptidase, lipase, lactase, phytase, and cellulase. These enzymes improve the overall bioassimilation in the digestive tract but are still not proven to increase bloodstream bioavailability. 
The enzymes break the bigger substances in some foods into smaller molecules so they can go through the rest of the digestive tract more easily.