How Digestive System Works

To gain a thorough understanding of how the digestive system works, let’s take a guided tour starting at the brain and ending at the colon.


Digestion begins before we even put food into our mouths. Any sound, sight, odor, taste, or texture associated with food can trigger the body to prepare for what will arrive. Digestive juices, saliva, enzymes, and digestive hormones begin to flow in anticipation.

In addition, the body “revs up” to prepare for the work of digestion, and the heart rate and blood flow can change. Although this phase of digestion only lasts a short time, it emphasizes the importance of eating in a relaxed manner and of appreciating the food you are about to ingest.

Some people find that taking time to say grace and to look at and smell the food, as well as making a special time and place for eating, can dramatically enhance their total digestive function.


The main function of the mouth is to chew and liquefy food. The salivary glands, located under the tongue, produce saliva, which softens food, begins dissolving soluble components, and helps keep the mouth and teeth clean. Saliva contains amylase, an enzyme for splitting carbohydrates.

Only a small percentage of starches are digested by amylase, but if you keep a piece of bread in your mouth for a long time, you can begin to taste the increased sweetness that comes from splitting the starch into simple sugars. Chewing also stimulates the parotid glands, behind the ears in the jaw, to release hormones that stimulate the thymus to produce T-cells, which are the core of the protective immune system.

Healthy teeth and gums are critical for proper digestion. Many people eat too fast; they barely chew their food at all and then wash it down with liquids. So the stomach receives chunks of food instead of mush. This undermines the function of the teeth, which is to increase the surface area of the food.

Fast eaters often complain of indigestion or gas. In May All Be Fed, John Robbins describes three men who survived in a concentration camp during World War II by chewing their food very well. Simply by chewing food thoroughly we can enhance digestion and eliminate some problems of indigestion.


The esophagus is the tube that passes from the mouth to the stomach. Here, peristalsis begins to push the food along the digestive tract. Well-chewed food passes through the esophagus in about six seconds, but dry food can get stuck and take minutes to pass.

The cardiac or esophageal sphincter—a little door at the bottom of the esophagus—separates the esophagus from the stomach, keeping stomach acid and food from coming back up. It remains closed most of the time, opening when a peristaltic wave, triggered by swallowing, relaxes the sphincter. The most common esophageal problems are heartburn (also called gastric reflux) and hiatal hernia.


The stomach chops, dices, and liquefies as it changes food into a soupy liquid called chyme, which is the beginning of the process of protein digestion. The stomach is located under the rib cage, just below the heart. Protein molecules are composed of chains of amino acids—up to two hundred amino acids strung together.

Hydrochloric acid (HCl), produced by millions of parietal cells in the stomach lining, begins to break apart these protein chains. HCl also kills microbes that come in with food, effectively sterilizing it. HCl is so strong that it would burn our skin and clothing if spilled.

Yet, the stomach is protected by a thick coating of mucus (mucopolysaccharides), which keeps the acid from burning through the stomach lining. Prostaglandins, small chemical messengers, help keep the mucous layer active by sending messages to replace and repair the stomach lining and provide a protective coating.

When this mucous layer breaks down, HCl burns a hole in the stomach lining, causing a gastric ulcer. The stomach also makes pepsin, a protein-splitting enzyme that cuts the bonds between specific amino acids, breaking them down into short chains of just four to twelve. The stomach also produces small amounts of lipase, enzymes that digest fat.

Most foods are digested and absorbed farther down the gastrointestinal tract, but alcohol, water, and certain salts are absorbed directly from the stomach into the bloodstream. That’s why we feel the effects of alcohol so quickly. Food stays in the stomach two to four hours—less with a lowfat meal, more with a high-fat or high-fiber meal.

When the stomach has finished its job, chyme has the consistency of split pea soup. Over several hours, it passes in small amounts through the pyloric valve into the duodenum, the first twelve inches of the small intestine. Chronic stress lengthens the amount of time that food stays in the stomach, while short-term stress usually shortens the emptying time.

Vitamin B12 and Intrinsic Factor

Before vitamin B12 even had a name, scientists knew that there was something in food that joined with something in the stomach that helped its absorption. They named these two substances intrinsic factor (manufactured in our stomach) and extrinsic factor (from food), which is now called vitamin B12.

Vitamin B12 is essential for blood formation, energy, growth, and cell division and function. Intrinsic factor is made in the stomach in the parietal cells, and binds vitamin B12 so that it can be readily absorbed in the intestines. Hydrochloric acid is also produced by the parietal cells.

As the parietal cells become less efficient, the production of both hydrochloric acid and intrinsic factor falls. As we age, the ability to manufacture HCl decreases. Intrinsic factor is likewise decreased and vitamin B12 deficiencies occur. Many elderly people have vitamin B12 deficiencies that affect the body’s ability to get oxygen into each cell.

The main symptoms are dementia, depression, nervous system problems, muscle weakness, and fatigue. Many people benefit from vitamin B12 injections, under a physician’s care, even though many do not have low serum B12 levels or pernicious anemia (anemia caused by B12 deficiency).

B12 shots or sublingual tablets can dramatically increase energy levels and decrease the symptoms listed. The most common problems associated with the stomach are gastric ulcers and underproduction of hydrochloric acid.

Small Intestine

The small intestine is hardly small. If this coiled-up garden hose were stretched out, it would average fifteen to twenty feet long. If spread flat, it would cover a surface the size of a tennis court.

In the small intestine, food is completely digested and nutrients are absorbed through hundreds of small fingerlike folds called villi, which are located in the intestinal wall and are covered, in turn, by millions of microvilli. (Think of them as small loops on a velvety towel that then have smaller threads projecting from them.)

The villi and microvilli are only one cell layer thick but perform multiple functions of producing digestive enzymes, absorbing nutrients, and blocking absorption of substances that aren’t useful to the body. The intestinal lining repairs and replaces itself every three to five days.

The sloughed material contains enzymes and fluids that are recycled to help digestion. The intestinal wall has a paradoxical function: it allows nutrients to pass into the bloodstream while blocking the absorption of foreign substances found in chemicals, bacterial products, and other large molecules found in food.

Some foods we eat and medications we use cause the intestinal wall to lose the ability to discern between nutrients and foreign substances. When this occurs, there is a problem of increased intestinal permeability, commonly known as leaky gut syndrome. This syndrome contributes to skin problems, food sensitivities, osteoarthritis, migraine headaches, and chronic fatigue syndrome.

The small intestine has three parts: the duodenum, the jejunum, and the ileum. The duodenum is the first twelve inches of the small intestine, the jejunum is the next 40 percent, and the ileum is the last segment. Each nutrient is absorbed at specific parts of the small intestine.

For instance, the duodenum has an acidic environment that facilitates absorption of some nutrients, including calcium, copper, iron, folic acid, thiamine, manganese, vitamins A and B2, and zinc. People with low hydrochloric acid levels might become deficient in one or more of these nutrients because they need acid for absorption.


The pancreas has two main roles. First, it produces digestive enzymes and insulin. When food passes from the stomach to the duodenum, the pancreas secretes bicarbonates, essentially baking soda, which neutralizes the acidity of the chyme so it won’t burn the tissues of the intestines.

Then, it manufactures and secretes specific enzymes that digest fats, carbohydrates, and protein. These enzymes are lumped into three categories: lipase, amylase, and protease. Lipase breaks fats into fatty acids and glycerol; amylase splits carbohydrates into simple sugars; and protease digests the links between amino acids from protein.

Once digested, these nutrients can be absorbed into the bloodstream and used by the cells. Low secretion of pancreatic enzymes can also lead to nutritional deficiencies. For example, vitamin B12 requires proteinsplitting enzymes to separate it from its carrier molecule, so poor pancreatic function can lead directly to vitamin B12 deficiency.

The second role of the pancreas is hormonal regulation of blood sugar levels. When the blood sugar is too high, the pancreas secretes insulin that signals the cells to store glucose. When this mechanism fails, people develop diabetes.

Gut-Associated Lymphatic Tissue (GALT)

Current research indicates that 70 percent of the immune system is located in or around the digestive system. The mucosal surface of the gut is only one cell thick. Underneath this is the gutassociated lymphatic tissue (GALT). It must continually distinguish between friend and foe in the foods we eat and in the gut bacteria.

When the digestive system is presented with a foreign substance, an antigen, specialized cells called M-cells carry the antigen to the lining of the digestive tract. There they are “checked out,” or sampled, by specialized cells called Peyer’s patches in the intestinal lining.

These cells in turn alert B- and T-cells to begin processing the antigens. The B- and T-cells carry the antigens back to the intestinal mucosa, where they are gobbled up by macrophages, part of the cell-mediated immune system.

Secretory IgA (sIgA) antibodies, which are like sentinels on constant alert for foreign substances, are also present in the gut mucosa. Their arousal signals cytokines, which begins the inflammatory process designed to rid our bodies of antigenic materials.

When microbes enter the digestive system, they are confronted with several nonspecific and antigen-specific defense mechanisms including: peristalsis, bile secretion, hydrochloric acid, mucus, antibacterial peptides, and IgA. This stops most microbes and parasites from infecting the body.

Those that do get through this defense system are recognized by toll-like receptors (TLRs). When disease-causing microbes get through, the TLRs stimulate production of inflammatory cytokines by activation of NF-kappa B, triggering cytokine production and inflammation in the gut.

It is believed that the constant exposure to microbes in infancy and early childhood contributes to the health and responsiveness of the adult immune system. This theory is called the “Hygiene Hypothesis.” In our culture, we don’t challenge the immune system enough.

We have improved sanitation, low bacterial availability in the foods we eat because of preservatives and food processing, decreases in consumption of fermented foods, fewer childhood infections, increased use of antibiotics, and routine use of vaccinations. Children who have little challenge to microbes are at risk for allergy, eczema, and asthma, which may continue throughout a lifetime.

Gut Serotonin

Serotonin is best known for its role in the brain, but 95 percent of our serotonin is manufactured in the gut. Without adequate amounts, we have insomnia and are depressed. Many selective serotonin reuptake inhibitor (SSRI) drugs are on the market to help keep serotonin in the synapses for a longer period of time. The most well-known of these is Prozac.

Serotonin in the gut plays a role in peristalsis, smooth muscle contraction, and mucosal secretions. A second gut hormone, called enterochromaffin cells (EC cells) also activate the gut nerves and can cause nausea that is associated with chemotherapy and possibly the bloating and pain associated with irritable bowel syndrome.


The gallbladder is a pear-shaped organ that lies just below the liver. Its function is to store and concentrate bile produced by the liver. Bile emulsifies fats, cholesterol, and fat-soluble vitamins by breaking them into tiny globules. These create a greater surface area for the fat-splitting enzymes (lipase) to act on during digestion.

When we eat, the gallbladder and liver release bile into the common duct, which connects the liver, gallbladder, and pancreas to the duodenum. Between meals, the gallbladder concentrates bile. The most common problem of the gallbladder is gallstones. When bile becomes too concentrated, stones might form, which can cause pain, nausea, and discomfort. Gallbladder disease is directly related to diet.


The liver is the most overworked organ in the body because it plays many roles. It manufactures bile to emulsify fats for digestion; it makes and breaks down many hormones, including cholesterol, testosterone, and estrogens; it regulates blood sugar levels; and it processes all food, nutrients, alcohol, drugs, and other materials that enter the bloodstream and lets them pass, breaks them down, or stores them.

The job of neutralizing environmental pollution inside the body is no small task—one that the liver never evolved to handle. Yet, the liver can lose as much as 70 percent of its capability and not show diagnosable liver disease. The four-and-a-half-pound liver manufactures thirteen thousand chemicals and has two thousand enzyme systems, plus thousands of synergists that help with body functions.

With these chemicals and enzymes, it “humanizes” nutrients so that the cells can use them. Practically all vitamins and minerals we take in need to be enzymatically processed by the liver before we can use them. If the liver is too congested to enzymatically process these nutrients, we do not get the benefit.

Bile, manufactured by the liver and stored by the gallbladder, buffers the intestinal contents because of its high concentration of bicarbonates. It also emulsifies fats. Bile is a soap-like substance made of bile salts, cholesterol, and lecithin. It makes fats more water soluble, increasing their surface area so that the enzymes can split them for the cells to use.

The liver has three lobes: main, left, and lower. The main lobe organizes and humanizes nutrients. It is the main chemical factory, producing enzymes and chemicals necessary for body functions. The left lobe regulates and maintains body functions. People with toxic left lobes are often environmentally sensitive or panallergic— allergic to nearly everything.

Many times, allergic people crave what they are sensitive to. The body gets used to having nicotine, alcohol, wheat, dairy, or whatever, and when we remove it, the body’s balance is disturbed. The left lobe works to maintain body homeostasis (staying the same) without the “missing” substance.

The craving is, in some part, the liver’s way of trying to get us what we “need.” As Jack Tips writes in The Liver Triad, “As long as toxic residues from these substances are present in this lobe, the body will get a subtle signal to continue the addiction, to want to respond to allergens.”

The lower lobe is where the essential fatty acids and fat-soluble vitamins A, D, E, and K are stored so the liver and other glands can produce cholesterol and hormones. Here, the liver also stores environmental toxins such as radioactive substances, pesticides, herbicides, food preservatives, and dyes.

The liver will detoxify what it can, but if it can’t break down a particular substance, it stores it in the lower lobe and in tissues throughout the body. It is important to detoxify the liver on a regular basis, perhaps twice a year, to help maintain its function.