In humans, digestion begins in the mouth, which converts food into a soft, moist mass. The mouth opens up the body to an environment filled with bacteria, fungi, dust, etc. It is estimated that more than 400 bacterial species reside in the oral cavity. The oral mucosa (or lining of the mouth), along with saliva, act as a primary defense for protection against a variety of microbes. The flow of saliva has a mechanical effect, flushing microorganisms from mucosal and tooth surfaces.

The muscular tongue pushes the food against the teeth, which cut, chop, and grind the food. Glands in the cheek linings secrete mucus, which lubricates the food, making it easier to chew and swallow. The design pattern of teeth is too intricate that the shape, contours, and angulation of teeth make it possible to grind and tear, whereas without proper angulation and contour, teeth would simply shred and poke holes. The ideal fit of upper and lower teeth with two cogs of a wheel coming together at precisely the right point. The front teeth, which tear and shred food, can exert a force of up to 80 pounds. while the grinding molars can apply 100-250 pounds of force against food particles!

Three pairs of glands empty saliva into the mouth through ducts to moisten the food. During the day, these glands produce from 1 to 1 1/2 quarts of saliva. Saliva functions as a solvent in cleansing the teeth and dissolving food chemicals so they can be tasted. Saliva also contains enzymes, which digest starch, and mucus, which lubricates the pharynx to facilitate swallowing. Saliva contains amylase enzyme, which digests starch to maltose. By the time thoroughly chewed food reaches the stomach, where the acidity inactivates amylase, the average chain length of starch has been reduced from several thousand to fewer than eight glucose units. Saliva also contains a wide spectrum of antimicrobial agents such as lactoferrin, lysozyme and salivary peroxidase. Saliva also has a cleansing action as its constant flow helps to dissolve and remove food particles from the teeth.

The presence of food in the pharynx stimulates swallowing, which squeezes the food into the esophagus. The esophagus is a muscular tube of about 10 inch long that connects the mouth to the stomach. A circular muscle called the esophageal sphincter separates the esophagus and the stomach. As food is swallowed, this muscle relaxes, forming an opening through which the food can pass into the stomach. Then the muscle contracts, closing the opening to prevent food from moving back into the esophagus. The esophageal sphincter is the first of several such muscles along the alimentary canal. These muscles act as valves to regulate the passage of food and keep it from moving backward. Food travels the length of the esophagus in 2 to 3 seconds.

Stomach is a J-shaped, expandable sack, located on the left side of the upper abdomen. It has active muscles that expand and contract depending on the quantity of food in the stomach. This contraction causes mechanical breakdown of the food. The purpose of this breakdown is to increase the available surface area for subsequent chemical activity. A normal stomach can expand to hold about 2 liters (~ ½ gallon) of food.

The gastric glands of the stomach secrete juices that perform chemical breakdown, partly digesting the proteins. Gastric juices in the stomach are secreted at a rate of 2-3 quarts/day. These juices contain primarily hydrochloric acid (HCl) and digestive enzymes. HCl makes the stomach a very acid environment with a pH factor between 1.5 and 3.0. This acidic environment serves two functions: i) it denatures the proteins and ionizes the minerals; and ii) it kills food-borne microorganisms.

Two primary enzymes are also present in the gastric juices. The first is pepsin, which aids in the hydrolysis of proteins. Pepsin begins breaking down of complex food proteins into their simpler forms. The acidic milieu created by HCl is critical for pepsin activity. The second enzyme in gastric juice is lipase, which aids in the hydrolysis of fats. Lipase starts the digestion of fats and breaks them into glycerol and fatty acids. The lipase activity is optimum at neutral pH in contrast to acidic environment required for pepsin enzyme. These enzymes, along with the gastric juices, are mixed into the food by the mechanical actions of the stomach. Stomach secretes mucus to protect itself from being digested by its own acid and enzymes.

Gastric Motility

The movement and flow of chemicals into the stomach are controlled by both the autonomic nervous system and by various hormones. The hormone gastrin causes an increase in HCl secretion from the parietal cells, and pepsinogen from chief cells in the stomach. It also causes increased motility in the stomach. It is inhibited by a pH normally <4 (high acid), as well as the hormone somatostatin. Cholecystokinin (CCK) has most effect on the gall bladder contractions, but it also decreases gastric emptying and increases release of pancreatic juice which is alkaline and neutralizes the chyme. In a different and rare manner, secretin, produced in the small intestine, has most effects on the pancreas, but will also diminish acid secretion in the stomach. Gastric inhibitory peptide (GIP) and enteroglucagon decrease both gastric secretion and motility. Other than gastrin, rest of the above hormones all act to turn off the stomach action. Stomach needs to push food into the small intestine only when the intestine is not busy. When the intestine is full and busy in digesting the food, stomach acts as storage for food.

Stomach empties at a slow rate of about 3/100 ounce for each peristaltic wave. At 3 waves/min, it can take up to 5-h for 2-lbs of food to leave the stomach.The emptying time of the stomach also varies with the type of food present. Water and liquids leave the stomach most rapidly. Carbohydrates empty more quickly than proteins; proteins, in turn, leave the stomach more quickly than fats. Within 5-min after fat enters the stomach, the hormone – enterogastrone, enters the bloodstream and travels to the stomach and inhibits the motion of the stomach and causes it to empty at a much slower rate. Not all foods undergo the same digestive processes in the stomach, and not all foods leave the stomach at the same rate. Proteins digest in an acid environment, while fats need a neutral environment. Carbohydrates leave the stomach at a faster rate than proteins.

Although the absorption is mainly a function of the small intestine, absorption of certain small molecules also occurs in the stomach through its lining. This includes: Water, if the body is too dehydrated; simple sugars (eg. Glucose), medication (eg. aspirin), and amino acids.

Stomach acts as a nutrition sensor. It can "taste" sodium glutamate using glutamate receptors and this sensory message is passed to the lateral hypothalamus and limbic system in the brain as a palatability signal through the vagus nerve. The stomach can also sense independently to tongue and oral taste receptors glucose, carbohydrate, proteins and fats. This allows the brain to link nutritional value of foods to their tastes [Uematsu et al 2009 & 2010).

Most digestion, as well as absorption of digested food, occurs in the small intestine. This narrow, twisting tube, about 2.5 cm (1 in) in diameter, fills most of the lower abdomen, extending about 6 m (20 ft) in length. Over a period of 3 to 6 hours, peristalsis moves chyme through the duodenum into the next portion of the small intestine, the jejunum, and finally into the ileum, the last section of the small intestine.

Micro-Villi

The small intestine’s capacity for absorption is increased by millions of fingerlike projections called villi, which line the inner walls of the small intestine. Each villus is about 0.5 to 1.5 mm (0.02 to 0.06 in) long and covered with a single layer of cells. Even tinier fingerlike projections called microvilli cover the cell surfaces. This combination of villi and microvilli increases the surface area of the small intestine’s lining by about 150 times, multiplying its capacity for absorption.

The villi of the intestine move back and forth, like thousands of tiny tentacles, passing through the food as it is moved along the intestinal tract. The villi play an important role in the absorption of food from the small intestine. Through the center of each villi is one or more fine white vessels called lacteals. The lacteals are part of the lymphatic system. Their principal function is probably the absorption of fat. As food passes through the small intestine, it is taken up, or absorbed, by structures in the wall of the intestines, especially the villi, and is then secreted into the lacteals. Beneath the villi’s single layer of cells are capillaries (tiny vessels) of the bloodstream and the lymphatic system. These capillaries allow nutrients produced by digestion to travel to the cells of the body. Simple sugars and amino acids pass through the capillaries to enter the bloodstream. Fatty acids and glycerol pass through to the lymphatic system.Blood from the intestines containing these products of digestion is collected in the portal vein, which is connected to the liver.

The liver removes the excess glucose from the blood (glucose being one of the end-products of digestion) and stores it as glycogen, to be used later in normalizing the blood-sugar level and for supplying energy. It also attempts to detoxify harmful elements in the food (such as pesticides), and regulates the level of nutrients available to the body. The liver is one of the master organs in the body. It receives all the end-products of digestion. The bulk that remains behind after the vital elements are extracted by the villi in the intestine and sent to the liver is then pushed down toward the large intestine. Normally, most of the contents of the intestines have been absorbed by the time the food reaches the middle of the jejunum segment of the intestine, or about 3 feet along the 9 feet of tubing that makes up the small intestine. The tone and motility of the small intestine is increased by foods served at room temperature, fibrous foods, and high-carbohydrate, low-fat foods. Movement is slowed by cold, dry, and high-fat foods.

Duodenum

The duodenum is the smallest segment of the intestine, being only 8 inches long. Food travels through the small intestine by peristalsis (weak contracting waves of motion) that propels the food toward the large intestine. The other two segments of the small intestine are the jejunum, which is 3 feet long and connects the duodenum to the ileum, the final 3 feet of the small intestine. Peristalsis is a manifestation of two major reflexes within the enteric nervous system that are stimulated by a bolus of foodstuff in the lumen.

Liver and Pancreas

During this time, the liver secretes bile into the small intestine through the bile duct. The liver holds the distinguished honor of being the largest glandular organ in the human body. Bile breaks large fat globules into small droplets, which enzymes in the small intestine can act upon. Pancreatic juice, secreted by the pancreas, enters the small intestine through the pancreatic duct. Pancreatic juice contains enzymes that break down sugars and starches into simple sugars, fats into fatty acids and glycerol, and proteins into amino acids. Glands in the intestinal walls secrete additional enzymes that break down starches and complex sugars into nutrients that the intestine absorbs. Structures called Brunner’s glands secrete mucus to protect the intestinal walls from the acid effects of digestive juices.

A watery residue of indigestible food and digestive juices remains unabsorbed. This residue leaves the ileum of the small intestine and moves by peristalsis into the large intestine, where it spends 12 to 24 hours.

The small intestine joins the colon in the region of the right groin. The large intestine forms an inverted ‘U’ over the coils of the small intestine. It starts on the lower right-hand side of the body and ends on the lower left-hand side. The large intestine is 1.5 to 1.8 m (5 to 6 ft) long and about 6 cm (2.5 in) in diameter. At this juncture is the ileo-cecal valve to control the speed of passage of substances from the small intestine. The ileo-cecal valve opens into a pouch in the colon known as the cecum, the first receptacle for waste residue. At the tip of the cecum is the appendix. Due to the appendix's position near the waste receptacle, toxins from a diet high in meat, heavy starches, etc. can contribute to its inflammation which may result in a condition known as appendicitis. From the cecum, the large intestine ascends on the right side to the middle of the abdomen, then crosses to the left side and descends again. These three sections are called the ascending, transverse and descending colons.

The large intestine serves several important functions. It absorbs water, about 6 liters (1.6 gallons) daily, as well as dissolved salts from the residue passed on by the small intestine. If an excess of water is expelled with the feces, then a condition known as diarrhea exists. Any irritation in the stomach and small intestine due to unsuitable food or inflammation develops the onset of diarrhea. In such condition, the colon expels its entire waste residue upon entry without holding it for water reabsorption. On the other hand, if the waste residue moves too slowly through the colon, then excessive water is reabsorbed and the feces become hardened, which leads to constipation.

In addition, bacteria in the large intestine promote the breakdown of undigested materials and synthesize several vitamins, notably vitamin K, which the body needs for blood clotting. The large intestine moves its remaining contents toward the rectum, which makes up the final 15 to 20 cm (6 to 8 in) of the alimentary canal. The rectum stores the feces – waste material that consists largely of undigested food, digestive juices, bacteria, and mucus – until elimination.

The human body has been designed so that pelvic muscles can be employed in order to aid in removing waste from the body. During the act of defecation the longitudinal rectal muscles contract to increase rectal pressure, and the internal and external anal sphincter muscles relax. Excretion is aided by contractions of abdominal and pelvic skeletal muscles, which raise the intra-abdominal pressure and help push the feces from the rectum through the anal canal and out the anus. When sphincters between the rectum and anus relax, the feces pass out of the body.

Rectum is the terminal portion of the large intestine and functions for storage of the feces, the wastes of the digestive tract, until these are eliminated. The external opening at the end of the rectum is the anus. The anus has two sphincters, one voluntary and one involuntary. The pressure of the feces on the involuntary sphincter causes the urge to defecate and the voluntary sphincter controls whether a person defecates or not.

Finally, the journey of food through the body is completed. Many healthy individuals process the food from the mouth to the anus in about 16 to 24-h. Most adults eating a conventional diet, however, generally take from forty-eight to seventy-two hours for their food to complete its journey. Much of this added delay is due to incompatible food combinations and lack of colon vitality.

GI tract Transit time: The transit time for food or other ingested materials to pass through the GI tract depends on several factors and roughly takes 2.5 to 3-h after a meal for 50% of stomach contents to empty into the intestines, while total emptying of the stomach takes 4 to 5-h. Subsequently, 50% emptying of the small intestine takes 2.5 to 3-h. Finally, transit through the colon takes 30 to 40-h [Camilleri et al 1989]. These estimates of average GI tract transit times vary among individuals, as well as, within the same person at different times and after separate meals. First, there is considerable variability in transit times through different sections of the GI tract among healthy people. Second, the time required for material to move through the GI tract is markedly affected by the composition of the meal. Finally, transit time is influenced by factors such as psychological stress, gender and reproductive status [Charles et al 1995, Degen and Phillips 1996].

GI tract transit studies have demonstrated two related phenomena important to understanding this process: i) substances do not move uniformly through the GI tract, and ii) materials do not leave segments of the digestive tube in the same order as they arrive. In other words, when the meal is a typical mixture of chemically and physically diverse materials, certain substances in such mixture show accelerated transit while others are retarded in their flow downstream [Metcalf et al 1987].