The stomach is a large organ, located under the rib cage, just below the heart.

It has three layers of muscle, running up and down, across and crosswise. As these muscles contract, the food mixture is churned up into a soupy liquid called chyme. The stomach adds quantities of the digestive enzyme pepsin and strong hydrochloric acid to the churning mixture, which helps to break down dietary protein.

Protein molecules are composed of chains of amino acid – up to 200 amino acids strung together. Hydrochloric acid, produced by millions of parietal cells in the stomach lining, begins to break apart these protein chains. Hydrochloric acid also kills microbes that come in with food, effectively sterilising it. Hydrochloric acid 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 keep the acid from burning through the stomach lining.

Prostaglandins, small chemical messengers, help keep the mucus layer active by sending messages to replace and repair the stomach lining and provide a protective coating.

If acid production is excessive, however, or if the barrier is weak, the stomach lining may be eroded. The result is an 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 4 to 12. The stomach also produces small amounts of lipase, enzymes that digests fat. Most foods are digested and absorbed further 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.

Although a few substances, such as aspirin, may enter the bloodstream directly through the stomach walls, most food is stored here until contractions of the smooth muscle wall pump it into the small intestine. It may take between two and four hours (or longer) for an average-sized meal to be pumped into the small intestine. Even when the stomach is empty, the muscles continue their steady pumping action.

The wavelike contractions, called peristalsis, create the familiar pain that signal “hunger” to the brain. The growling sound made by the continuous contractions tends to be louder when the stomach is empty. Anxiety causes an even louder noise because the smooth muscle is responsive to stress.

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 12 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 have 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 hydrochloric acid decreases. Intrinsic factor is likewise decreased and vitamin B12 deficiencies can 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 anaemia (anaemia 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

Most of the serious business of digestion and absorption occurs in the long, narrow, small intestine.

The small intestine is hardly small. If this coiled-up garden hose was stretched out, it would average 5-7 metres 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.

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 are not useful to the body.

The intestinal lining repairs and replaces itself every 3 to 5 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 30cm of the small intestine, the jejunum is the next 40%, 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 require acid for absorption

The food mixture first enters the duodenum, another likely place for ulcers to develop because the mixture is still acidic.

The major work of digestion begins here with action from certain hormones. One hormone, known as cholecystokinin, or CCK, draws in bile from the gallbladder to make fat more digestible. This same hormone also draws juices from the pancreas to calm the acidity left in the food mixture and to aid digestion of fat, protein, and carbohydrates.

The food mixture travels along the small intestine allowing time for refined processing and absorption. Proteins are split by various enzymes into individual amino acids; carbohydrate becomes simple sugar; and fat becomes glycerol and fatty acid. In this form, food can be absorbed by the body.

As the nutrients pass by, the villi pick them out and transport them into the bloodstream.

The digestive system now begins to interact with another body system, the circulatory system. Nutrients travel through the bloodstream to the liver, a giant chemical factory that is the key organ of human metabolism.

The liver works around the clock to secrete bile, make various proteins, and remove toxic substances from ingested food. Blood that has circulated through the liver is ready to be used as fuel by body cells. If the liver fails, the body dies.

Gut Associated Lymphatic Tissue (GALT)

Current research indicates that 70% 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 gut associated 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, specialised cells called M-cells carry the antigen to the lining of the digestive tract. There, they are “checked out”, or sampled, by specialised 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 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 read our bodies of antigenic materials.

When microbes enter the digestive system, they are confronted with several non-specific antigen-specific defence 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 defence system are recognised 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 sufficiently. 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.

Serotonin

Serotonin is best known for its role in the brain, but 95% of our serotonin is manufactured in the gut. Without adequate amounts, we may have insomnia and become 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.