The Encyclopedia of Natural Medicine, 3rd Ed.

Digestion and Elimination



If we are to gain the nutritional benefits from foods, they must be properly digested, absorbed, and eliminated. The best food in the world will go to waste if the body is unable to process it. Fortunately, the human digestive system is quite efficient in extracting the necessary nutrients from foods.

The major functions of the gastrointestinal system are to break down and absorb nutrients. The digestive system extends from the mouth to the anus. It consists of the gastrointestinal tract and its appendage organs, such as salivary glands, the liver and gallbladder, and the pancreas.

Digestion occurs as a result of both mechanical and chemical processes. The mechanical processes of digestion are brought about by grinding and crushing the food mass and mixing it with digestive juices during propulsion through the digestive tract. The digestive juices are responsible for the chemical breakdown of food. The active compounds in the digestive juices are primarily hydrochloric acid and enzymes.

The Digestive Process

The digestive process begins in the mouth. Chewing food thoroughly is the first step toward getting the most from the food you eat. Chewing signals other components of the digestive system to get ready to go to work; it also allows food to mix with saliva. Saliva contains the enzyme salivary amylase to break down starch molecules into smaller sugars. Once the food has been chewed, it is transported through the esophagus into the stomach.

Food is broken down in the stomach by mechanical as well as chemical means. The stomach churns and gyrates to promote the mixing of the food with its digestive secretions, including hydrochloric acid and the enzyme pepsin. These factors are critical to proper protein digestion and mineral absorption. If hydrochloric acid secretion is insufficient or inhibited, proper protein digestion will not occur. Food remains in the stomach until it is reduced to a semiliquid consistency. In general, this process takes anywhere from 45 minutes to four hours. Once the food material leaves the stomach it is referred to as chyme.

It takes chyme approximately two to four hours to make its way through the 21-foot-long small intestine. The small intestine is divided into three segments: the duodenum is the first 10 to 12 inches, the jejunum is the middle portion and is about 8 feet long, and the ileum is about 12 feet long. The small intestine participates in all aspects of digestion, absorption, and transport of ingested materials. It secretes a variety of digestive and protective substances as well as receives the secretions of the pancreas, liver, and gallbladder.

Absorption of minerals occurs predominately in the duodenum; absorption of water-soluble vitamins, carbohydrates, and protein occurs primarily in the jejunum; and the ileum absorbs fat-soluble vitamins, fat, cholesterol, and bile salts.

Diseases involving the small intestine often result in malabsorption syndromes characterized by multiple nutrient deficiencies. Examples of common causes of malabsorption include celiac disease (gluten intolerance), food allergy or intolerance, intestinal infections, and Crohn’s disease.

The Pancreas

The pancreas produces enzymes that are required for the digestion and absorption of food. Each day the pancreas secretes about 1.5 quarts of pancreatic juice in the small intestine. Enzymes secreted include lipases, proteases, and amylases.

Lipases, along with bile, function in the digestion of fats. Deficiency of lipase results in malabsorption of fats and fat-soluble vitamins. Amylases break down starch molecules into smaller sugars. The salivary glands as well as the pancreas secrete amylase. The proteases secreted by the pancreas (trypsin, chymotrypsin, and carboxypeptidase) function in digestion by breaking down protein molecules into single amino acids. Incomplete digestion of proteins creates a number of problems for the body, including the development of allergies and formation of toxic substances during putrefaction (the breakdown of protein by bacteria).

As well as being necessary for protein digestion, proteases serve several other important functions. The proteases are largely responsible for keeping the small intestine free from bacteria, yeast, and parasites such as protozoa and worms. A lack of proteases or other digestive secretions greatly increases an individual’s risk of having an intestinal infection, including chronic candida infections of the gastrointestinal tract. The proteases also are important in the prevention of tissue damage during inflammation, the formation of fibrin clots, and the deposition of immune complexes in body tissues.

The Liver and Biliary System

The liver manufactures bile, an extremely important substance in the absorption of fatty acids and fat-soluble vitamins. Bile produced by the liver is either secreted into the small intestine or stored in the gallbladder. Bile also plays an important role in making the stool soft by promoting the incorporation of water into the stool. Without enough bile, the stool can become quite hard and difficult to pass.

Like pancreatic enzymes, bile also serves to keep the small intestine free from microorganisms. Each day about one quart of bile is secreted into the small intestine. About 99% of what is excreted in the bile is reabsorbed in people who consume a low-fiber diet.

When additional bile acids are ingested, usually as ursodeoxycholic acid or ox bile salts, they are known to increase the output of bile and help promote a mild laxative effect. Another method of increasing the output of bile (a choleretic effect) is using herbal compounds such as milk thistle or artichoke extract.

The Colon

The colon is about five feet in length and functions in the absorption of water, electrolytes (salts), and, in limited amounts, some of the final products of digestion. The large intestine also provides temporary storage for waste products, which serve as a medium for bacteria. The health of the colon is largely determined by the types of foods that are eaten. In particular, dietary fiber is of critical importance in maintaining the health of the colon.


The Digestive System

As important as proper digestion is the effective elimination of waste products. A bowel movement every 12 to 24 hours is critical to good health. This frequency of elimination requires eating foods high in dietary fiber. Such a diet is rich in fruits, vegetables, whole grains, legumes, nuts, and seeds. A high-fiber diet increases both the frequency and the quantity of bowel movements, decreases the transit time of stools, decreases the absorption of toxins from the stool, and appears to be a preventive factor in several diseases that affect the colon, including constipation, colon cancer, diverticulitis, hemorrhoids, and irritable bowel syndrome.

Stress and Digestion

The autonomic nervous system controls all unconscious nervous activity. One part of it, the sympathetic nervous system, stimulates the fight-or-flight response; the other part, the parasympathetic nervous system, is responsible for the processes of digestion, repair, restoration, and rejuvenation. During stressful periods the sympathetic system dominates over the parasympathetic, directing the body to shunt blood and energy away from the digestive tract in favor of the skeletal muscles and brain. Regularly achieving a relaxed state (learning to calm the mind and body) is extremely important in relieving stress as well as improving digestion.


The term indigestion is often used by patients to describe heartburn and/or upper abdominal pain as well as a feeling of gassiness, swallowing, feelings of pressure or heaviness after eating, sensations of bloating after eating, stomach or abdominal pains or cramps, or fullness in the abdomen. The medical terms used to describe indigestion include functional dyspepsia (FD), non-ulcer dyspepsia (NUD), and gastroesophageal reflux disorder (GERD).

The dominant treatment of indigestion is the use of antacids and acid-blocker drugs. Acid-blocker drugs are divided into two general groups. One drug group is the older histamine-receptor antagonist drugs such as Zantac, Tagamet, and Pepcid AC. The other is the newer and more potent group of drugs called proton-pump inhibitors (PPIs), which includes Nexium, Prilosec, Protonix, Prevacid, and Aciphex. Use of antacid therapy, especially the newer drugs, is associated with an increased risk of osteoporosis, heart arrhythmias, intestinal infections, bacterial pneumonia, and multiple nutrient deficiencies. Most seriously, these drugs may increase the development of various gastrointestinal cancers.1 In regard to nutrient deficiencies, because the body uses gastric acid to release many nutrients from foods, people taking these acid-blocking drugs run the risk of multiple nutrient deficiencies. In particular, critical nutrients such as vitamin B12, magnesium, and iron are generally low in patients on long-term use of proton-pump inhibitors.

The stomach’s optimal pH range is 1.5 to 2.5, with hydrochloric acid being the primary stomach acid. The use of antacids and acid-blocker drugs will typically raise the pH above 3.5. This increase effectively inhibits the action of pepsin, an enzyme involved in protein digestion that can be irritating to the stomach. Although raising the pH can reduce symptoms, it must be pointed out that hydrochloric acid and pepsin are important factors in protein digestion. If their secretion is insufficient or their action inhibited, proper protein digestion and mineral disassociation will not occur. In addition, the change in pH can adversely affect the gut’s microbial flora, including promoting overgrowth of Helicobacter pylori, which has been linked to several stomach disorders. Therefore, it is important to use antacids wisely and sparingly. In addition, many nutrition-oriented physicians believe that it is not too much acid but rather a lack of acid that is the problem. Typically, in addressing indigestion, naturopathic physicians use measures to enhance rather than inhibit digestion. Commonly used digestive aids include hydrochloric acid, pancreatic enzyme preparations, and enteric-coated peppermint oil products.

General Considerations

Gastroesophageal reflux disorder (GERD) is most often caused by the flow of gastric juices up the esophagus (reflux esophagitis), leading to a burning discomfort that radiates upward and is made worse by lying down. Reflux esophagitis is most often caused by overeating. Other common causes include obesity, cigarette smoking, chocolate, fried foods, carbonated beverages (soft drinks), alcohol, and coffee. These factors either increase intra-abdominal pressure, thereby causing the gastric contents to flow upward, or decrease the tone of the esophageal sphincter. The first step in treating reflux esophagitis is prevention. In most cases this step simply involves eliminating or reducing the causative factor.

For occasional heartburn, antacids may well be appropriate. However, they should not be abused. The best choices are antacid preparations that also include alginate, a type of soluble fiber. In a very detailed review of all published clinical trials, it was shown that compared with the placebo response in GERD, which ranged between 37% and 64%, the relative benefit increase beyond that was only 11% with antacids, 41% with histamine-2 receptor antagonists, and 60% with alginate/antacid combinations.2 Be careful to avoid aluminum-containing antacids. Follow label instructions for any over-the-counter antacid preparation.

If heartburn is a chronic problem, it may be a sign of a hiatal hernia (outpouching of the stomach above the diaphragm). However, it is interesting to note that while 50% of people over the age of 50 have hiatal hernias, only 5% of patients with hiatal hernias actually experience reflux esophagitis.

Perhaps the most effective treatment of chronic reflux esophagitis and symptomatic hiatal hernias is to utilize gravity. The standard recommendation is to simply place 4-in. blocks under the bedposts at the head of the bed. This elevation of the head is very effective in many cases. Another recommendation is to use deglycyrrhizinated licorice (DGL, discussed below) to heal the esophagus,

A relatively new natural therapy for GERD is limonene, extracted from citrus fruit peel. Its mechanism of action is similar to enteric-coated peppermint oil in that it is thought to improve coordination of normal peristalsis. Surprisingly, taking 1,000 mg just once a week is helpful for many suffering from GERD.3 The typical recommendation, however, is one 1000-mg capsule, every other day, for 20 days, or a total of 10 doses.


Although much is said about hyperacidity conditions, a more common cause of indigestion is a lack of gastric acid secretion. Hypochlorhydria refers to deficient gastric acid secretion, and achlorhydria refers to a complete absence of gastric acid secretion.

There are many symptoms and signs that suggest impaired gastric acid secretion, and a number of specific diseases have been found to be associated with insufficient gastric acid output.412

Common Signs and Symptoms of Low Gastric Acidity

Bloating, belching, burning sensation, and flatulence immediately after meals

Sense of excessive fullness after eating

Indigestion, diarrhea, or constipation

Multiple food allergies

Nausea after taking supplements

Itching around the rectum

Weak, peeling, and cracked fingernails

Dilated blood vessels in the cheeks and nose


Iron deficiency

Chronic intestinal parasites or abnormal flora

Undigested food in stool

Chronic candida infections

Upper digestive tract gassiness

Diseases Associated with Low Gastric Acidity

Addison’s disease


Autoimmune disorders

Celiac disease

Dermatitis herpetiformis



Gallbladder disease

Graves’ disease


Hives (chronic)

Hyper- and hypothyroidism

Lupus erythematosus

Myasthenia gravis


Pernicious anemia


Rheumatoid arthritis


Sjogren’s syndrome



There is circumstantial evidence that the ability to secrete gastric acid decreases with age, but this association is now thought to be the result of increased overgrowth of the bacterium H. pylori in the stomach rather than any true effect of aging. Some older studies found low stomach acidity in over half of those over age 60.1315 The best method for diagnosing a lack of gastric acid is a special procedure known as the Heidelberg gastric analysis.16 This technique utilizes a electronic capsule attached to a string. The capsule is swallowed; once in the stomach, it measures the pH and sends a radio message to a receiver that records the pH level. After the test, the capsule is pulled up from the stomach by the string attached to it.

Not everyone can have detailed gastric acid analysis to determine the need for gastric acid supplementation. If you are experiencing any signs and symptoms of gastric acid insufficiency listed above, or have any of the diseases mentioned above:

• Begin by taking one tablet or capsule containing 500 to 600 mg hydrochloric acid at your next large meal. If this does not aggravate your symptoms, at every meal after that of the same size take one more tablet or capsule (two at the next meal, three at the meal after that, then four at the next meal).

• Continue to increase the dose until you reach seven tablets or when you feel warmth in your stomach, whichever occurs first. A feeling of warmth in the stomach means that you have taken too many tablets for that meal, and you need to take one less tablet for that meal size. It is a good idea to try the larger dose again at another meal to make sure that it was the HCl that caused the warmth and not something else.

• After you have found the largest dose that you can take at your large meals without feeling any warmth, maintain that dose at all of meals of similar size. You will need to take less at smaller meals.

• When you take multiple tablets or capsules, it is best to take them throughout the meal.

• As your stomach begins to regain the ability to produce the amount of HCl needed to properly digest your food, you will notice the warm feeling again and will have to cut down on the dose.

Helicobacter pylori Overgrowth

Overgrowth of the bacterium Helicobacter pylori in the stomach has been linked to GERD, achlorhydria, and hypochlorhydria, as well as peptic ulcer.17,18 The presence of H. pylori is determined by measuring the level of antibodies to H. pylori in the blood or saliva, or by culturing material collected during an endoscopy as well as measuring the breath for urea.

Low gastric output is thought to predispose to H. pylori colonization, and H. pylori colonization increases gastric pH, thereby setting up a positive feedback scenario and increasing the likelihood that the stomach and duodenum will be colonized with other organisms.19 This overgrowth chronically damages the lining of the stomach, resulting in progressive thinning and loss of the cells that secreted hydrochloric acid. Interestingly, it appears that habitual use of acid-blocking drugs may actually promote H. pylori overgrowth.20

If H. pylori gastritis leads to achlorhydria, the next obvious question is what factors lead to H. pylori gastritis. Consistent with its history, conventional medicine is obsessed with the infective agent rather than the host’s defense factors. Proposed protective factors against H. pylori–induced intestinal damage are maintaining a low pH and adequate antioxidant defense mechanisms.2123 Low levels of vitamin C, vitamin E, and other antioxidant factors in the gastric juice appear to lead to the progression of H. pylori colonization. The fact that H. pylori damages the stomach and intestinal mucosa by oxidation also contributes to the microorganism’s ulcer-causing potential.24 Furthermore, antioxidant status and gastric acid output appear to be the answer to the question why not everyone infected with H. pylori gets peptic ulcer disease or gastric cancer.

As for how to eradicate the organism as well as stimulate increased host defense factors, deglycyrrhizinated licorice (DGL) may prove useful. DGL has shown good results in healing both duodenal ulcers and gastric ulcers (discussed more fully in the chapter “Peptic Ulcer”). Rather than inhibit the release of acid, DGL stimulates the normal defense mechanisms that prevent ulcer formation. Specifically, DGL improves both the quality and the quantity of the protective substances that line the intestinal tract, increases the life span of the intestinal cell, and improves blood supply to the intestinal lining.

The active components of DGL are believed to be special flavonoid derivatives. These compounds have demonstrated impressive protection against chemically induced ulcer formation in animal studies. Several similar flavonoids have been shown to inhibit H. pylori in a clear-cut concentration-dependent manner.25 In addition, unlike antibiotics, the flavonoids were also shown to augment natural defense factors that prevent ulcer formation. The activity of flavone, the most potent flavonoid in the study, was shown to be similar to that of bismuth subcitrate. Bismuth is a naturally occurring mineral that can act as an antacid as well as exert activity against H. pylori. The best-known and most widely used bismuth preparation is bismuth subsalicylate (Pepto-Bismol); however, bismuth subcitrate has produced the best results against H. pylori and in the treatment of non-ulcer-related indigestion as well as peptic ulcers.26,27 In the United States, bismuth subcitrate preparations are available through compounding pharmacies [contact the International Academy of Compounding Pharmacists,, (800) 927-4227].

One of the advantages of bismuth preparations over standard antibiotic approaches to eradicating H. pylori is that while the bacterium may develop resistance to various antibiotics, it is very unlikely to develop resistance to bismuth. The usual dosage for bismuth subcitrate is 240 mg twice per day before meals. For bismuth subsalicylate the dosage is 500 mg (2 tablets or 30 ml standard-strength Pepto-Bismol) four times per day.

Bismuth preparations are extremely safe when taken at prescribed dosages and for periods of less than six weeks. Bismuth subcitrate may cause a temporary and harmless darkening of the tongue and/or stool. Bismuth subsalicylate should not be given to children recovering from the flu, chicken pox, or some other viral infection, as it may mask the nausea and vomiting associated with Reye’s syndrome, a rare but serious illness.

Another useful natural product that helps relieve symptoms of GERD is enteric-coated peppermint oil capsules (ECPO), which are coated to prevent their breakdown in the stomach. The primary use of ECPO has been in improving gastrointestinal function in individuals suffering from irritable bowel syndrome (IBS) (see the heading “Irritable Bowel Syndrome” on page 142 and also the chapter “Irritable Bowel Syndrome”), but it can also be helpful for NUD, GERD, and H. pylori.

Several clinical studies in patients with IBS featured the combination of peppermint oil and caraway oil. The results of these trials indicate that this combination produces better results than peppermint oil alone against symptoms of IBS. Recent studies also indicate that the combination of peppermint and caraway oil is more helpful in improving non-ulcer dyspepsia (NUD).28,29 In one double-blind study, 120 patients with NUD were given either the peppermint and caraway seed oil (ECPO) or the drug cisapride (Propulsid) for 4 weeks. The mean reduction of pain score was comparable in both groups (4.62 for ECPO, 4.6 for cisapride).29 Other symptoms of NUD improved in a similar fashion. Positive results were also found in H. pylori–positive individuals.

While enteric-coated peppermint and caraway oil is extremely safe at recommended levels, cisapride (Propulsid) was pulled from the market in July 2000 after being linked to 341 reports of heart rhythm abnormalities.

The usual dosage of enteric-coated capsules containing peppermint and caraway seed oil is 1 or 2 capsules (200 mg/capsule) up to three times per day between meals. Side effects are rare but can include allergic reactions (skin rash), heartburn, and if the dosage is too high a burning sensation upon defecation. There are no known drug interactions.

Pancreatic Insufficiency

Both physical symptoms and laboratory tests can be used to assess pancreatic function. Common symptoms of pancreatic insufficiency include abdominal bloating and discomfort, gas, indigestion, and the passing of undigested food in the stool. For laboratory diagnosis, most nutrition-oriented physicians use the comprehensive stool and digestive analysis.

Pancreatic insufficiency is characterized by impaired digestion, malabsorption, nutrient deficiencies, and abdominal discomfort. The most severe level of pancreatic insufficiency is seen in cystic fibrosis. Although cystic fibrosis is quite rare, mild pancreatic insufficiency is thought to be a relatively common condition, especially in the elderly.

Pancreatic enzyme products are the most effective treatment for pancreatic insufficiency and are also quite popular digestive aids. Most commercial preparations include pancreatin prepared from fresh hog pancreas.

The dosage of pancreatic enzymes is based on the level of enzyme activity of the particular product. The United States Pharmacopeia (USP) has set a strict definition for level of activity. A 1X pancreatic enzyme (pancreatin) product has in each milligram not less than 25 USP units of amylase activity, not less than 2 USP units of lipase activity, and not less than 25 USP units of protease activity. Pancreatin of higher potency is given a whole-number multiple indicating its strength. For example, a full-strength undiluted pancreatic extract that is 10 times stronger than the USP standard would be referred to as 8-10X USP. Full-strength products are preferred to lower-potency products, which are often diluted with salt, lactose, or galactose to achieve the desired strength (e.g., 4X or 1X). The dosage recommendation for an 8-10X USP pancreatic enzyme product would be 350 to 1,000 mg three times a day immediately before meals when used as a digestive aid and 10 to 20 minutes before meals or on an empty stomach when anti-inflammatory effects are desired.

Enzyme products are often enteric-coated, that is, they are often coated to prevent digestion in the stomach, so that the enzymes will be liberated in the small intestine. However, numerous studies have shown that non-enteric-coated enzyme preparations actually outperform enteric-coated products.30

Alternatives to pancreatin include plant enzymes (e.g., bromelain, papain) and enzymes extracted from various microbes or yeast (e.g., Aspergillus oryzae). These enzymes are more resistant to digestive secretions and are active across a broader pH range. One double-blind, crossover trial involving 17 patients with severe pancreatic insufficiency compared the effects of a non-enteric-coated pancreatic enzyme preparation (360,000 lipase units/day), an enteric-coated pancreatic enzyme preparation (100,000 lipase units/day), and a fungal enzyme preparation (75,000 lipase units/day).31 All three treatment preparations in both groups yielded significant reduction in total daily stool weight and total daily fecal fat excretion compared with controls. It is interesting to point out, however, that the fungal enzyme preparation produced similar benefit at three-fourths the dose of enteric-coated pancreatic enzyme and one-fifth the dose of non-enteric-coated pancreatic enzyme preparation.

Pancreatin and Food Allergies

Food allergies have been implicated as a causative factor in a wide range of conditions that affect many different parts of the body. The actual symptoms produced during an allergic response depend on the location of the immune system activation, the mediators of inflammation involved, and the sensitivity of the tissues to specific mediators. Since the gastrointestinal tract is a common site of immune system activation by a food allergy, it is not surprising that food allergies often produce gastrointestinal symptoms.

Both pancreatic insufficiency and hypochlorhydria play major roles in many cases of food allergies, particularly if a patient has multiple allergies. While starch and fat digestion can be carried out satisfactorily without the help of pancreatic enzymes, the proteases are critical to proper protein digestion. Incomplete digestion of proteins creates a number of problems for the body, including the development of food allergies. Typically individuals who do not secrete enough proteases will suffer from multiple food allergies.

In studies performed in the 1930s and 1940s, pancreatic enzymes were shown to be quite effective in preventing food allergies. The validity of this use has been verified in more recent studies.32

Small-Intestine Bacterial Overgrowth

The upper portion of the human small intestine is designed to be relatively free of bacteria. The reason is simple: when bacteria are present in significant concentrations in the duodenum and jejunum they compete with their host for nutrition. When bacteria (or yeast) get to the food first, problems can occur. The organism can ferment the carbohydrates and produce excessive gas, bloating, and abdominal distention. If this were not bad enough, the bacteria can also break down protein by the process of putrefaction to produce what are known as vasoactive amines. For example, bacteria and yeast contain enzymes (decarboxylases) that can convert the amino acid histadine to histamine and tyrosine to tyramine, in both cases causing inflammation and swelling. Even more dangerous-sounding (and smelly) are the compounds produced from the amino acids ornithine and lysine—namely, putrescine and cadaverine, respectively. All of these compounds are termed vasoactive amines to signify their ability to cause constriction and relaxation of blood vessels by acting on the smooth muscle that surrounds the vessels. In the intestinal tract, excessive vasoactive amine synthesis can lead to increased gut permeability (“leaky gut” syndrome), abdominal pain, altered gut motility, and pain. Vasoactive amines are also the primary cause of stool odor. The leaky gut syndrome results in the absorption of gut contents that normally do not enter the body and can lead to inflammation, joint pain, overwhelming of the immune and detoxification systems, and a variety of other symptoms.

Diagnosis of small-intestine overgrowth involves careful evaluation of the comprehensive digestive and stool analysis. There are also breath tests that measure hydrogen and methane after the administration of carbohydrates (lactulose and glucose). If there is small-intestine bacterial overgrowth, there will be higher than normal amounts of these gases.

Symptoms of small-intestine bacterial overgrowth are similar to those generally attributed to achlorhydria and pancreatic insufficiency—namely, indigestion and a sense of fullness (bloating)—but may also include symptoms generally associated with candida overgrowth (discussed below). More severe gastrointestinal symptoms may include nausea and diarrhea; arthritis may also be a result.33

The body has several protective measures that prevent bacterial overgrowth in the small intestine. The first is digestive secretions. In particular, hydrochloric acid, bile, and pancreatic enzymes play a critical role in preventing significant numbers of bacteria from migrating up the small intestine. Deficiencies in any of these may promote bacterial overgrowth. Normal peristalsis is another factor that prevents bacteria from overgrowing. Decreased motility in the small intestine due to a motility disorder (e.g., systemic sclerosis) or a meal high in refined sugar can contribute to small-intestine bacterial overgrowth. Under normal circumstances, secretory IgA, an antibody that protects and lines mucous membranes, is another safeguard. But low immune function, food allergies, stress, and other factors associated with a reduced level of secretory IgA can contribute to bacterial overgrowth in the small intestine. And finally, a weak ileocecal valve (the valve that separates the bacteria-rich colon contents from the ileum, the final segment of the small intestine) can lead to overpopulation of the small intestine with bacteria. A weak ileocecal valve is most often the consequence of long-term constipation or straining excessively at defecation; in both of these cases a low-fiber diet is most often responsible.

Factors Associated with Small-Intestine Bacterial Overgrowth

• Decreased digestive secretions due to:

  images Achlorhydria

  images Hypochlorhydria

  images Drugs that inhibit hydrochloric acid

  images Pancreatic insufficiency

  images Decreased bile output due to liver or gallbladder disease

• Decreased motility due to:

  images Scleroderma (progressive systemic sclerosis)

  images Systemic lupus erythematosus

  images Intestinal adhesions

  images Sugar-induced hypomotility

  images Radiation damage

• Low secretory IgA

• Weak ileocecal valve

Obviously, addressing the cause of the small-intestine bacterial overgrowth is the first step. The subject of decreased digestive secretions was discussed above. As for decreased motility, this most often is a result of a meal that is too high in sugar. The mechanism is simple: When blood sugar levels rise too rapidly, a signal is sent to the gastrointestinal tract to slow down. Since glucose is primarily absorbed in the duodenum and jejunum, the message most strongly affects this portion of the gastrointestinal tract. The result is that the duodenum and jejunum stop propelling chyme through the intestinal tract by peristalsis.

Restoring secretory IgA levels to normal involves eliminating food allergies (see the chapter “Food Allergy”) and enhancing immune function. Stress is particularly detrimental to secretory IgA. This effect offers an additional explanation as to why stressful events tend to worsen gastrointestinal function and food allergies.

One possible natural medicine to use in cases of small-intestine bacterial overgrowth is berberine. In addition to exerting broad-spectrum antibiotic activity (including activity against the yeast Candida albicans), berberine has been shown to inhibit decarboxylase, the bacterial enzyme that converts amino acids into vasoactive amines.34 Another natural medicine is pancreatic enzymes. As previously stated, the protein-digesting enzymes from the pancreas are largely responsible for keeping the small intestine free from bacteria and yeast as well as parasites such as protozoa and worms. A lack of proteases or other digestive secretions greatly increases an individual’s risk of having intestinal infections, including chronic candida infections of the gastrointestinal tract.

An overgrowth in the gastrointestinal tract of the usually benign yeast Candida albicans is now becoming recognized as a complex medical syndrome, called yeast syndrome or chronic candidiasis (see the chapter “Candidiasis, Chronic”). The overgrowth of candida is believed to cause a wide variety of symptoms in virtually every system of the body, with the gastrointestinal, genitourinary, endocrine, nervous, and immune systems being the most susceptible.

Elimination and Colon Function

Just as important as digestion is the elimination of waste from the body. The health and function of the colon (the large intestine) are very important to proper elimination. The colon is really not involved in digestion to any significant extent. It does function in the absorption of water and electrolytes (salts). But its primary role is to provide temporary storage for waste products and a site for the formation of stool. The health of the colon is largely determined by the amount of dietary fiber a person consumes. Without enough dietary fiber, waste material tends to accumulate.

Constipation affects more than 4 million people in the United States on a regular basis. This high rate of constipation translates to over $500 million in annual sales of laxatives. There are a number of possible causes of constipation, but the most common is a low-fiber diet. For more information, see the chapter “Constipation.”

Diverticular Disease

Diverticula are small sacs caused by the protrusion of the inner lining of the colon into areas of weakness in the colon wall. The term diverticulosis signifies the presence of diverticula in the colon. The incidence of diverticulosis increases with age, from less than 5% before age 40 to more than 65% by age 85. Most often the presence of diverticula causes no symptoms; however, if the diverticula become inflamed, perforated, or impacted, the condition is referred to as diverticulitis. Only about 20% of people with diverticulosis develop diverticulitis. Symptoms of diverticulitis include episodes of lower abdominal pain and cramping, changes in bowel habits (constipation or diarrhea), and a sense of fullness in the abdomen. In more severe cases, fever may be present along with tenderness and rigidity of the abdomen over the area of the intestine involved.

Treatment of diverticular disease involves a high-fiber diet. In severe cases of diverticulitis, an antibiotic may be warranted.

Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a very common condition in which the large intestine, or colon, fails to function properly. Estimates suggest that approximately 15% of the population suffers from IBS (also known as nervous indigestion, spastic colitis, mucous colitis, and intestinal neurosis).

IBS has characteristic symptoms that can include a combination of any of the following: abdominal pain and distension, more frequent bowel movements with pain, or relief of pain with bowel movements; constipation; diarrhea; excessive production of mucus in the colon; symptoms of indigestion such as flatulence, nausea, or anorexia; and varying degrees of anxiety or depression.

Irritable bowel syndrome is usually caused by a lack of dietary fiber in the diet, by food allergies, or by stress. Simply increasing the intake of plant food in the diet is effective in most cases. Also, in several double-blind studies, enteric-coated peppermint oil has been shown to relieve all symptoms of IBS in approximately 70 to 85% of cases within a two- to four-week period. IBS is discussed in more detail in the chapter “Irritable Bowel Syndrome.”


The human gastrointestinal tract is an incredibly complex ecosystem, with at least 500 different species of microflora normally found there. There are nine times as many bacteria in the gastrointestinal tract as there are cells in the human body. The type and number of gut bacteria play an important role in determining health and disease. A state of altered bacterial flora in the gut has become popularly known as dysbiosis. The term was first used by noted Russian scientist Élie Metchnikoff to reflect a state of living with intestinal flora that have harmful effects. He theorized that toxic compounds produced by the bacterial breakdown of food were the cause of degenerative disease. There is a growing body of research that supports and refines Metchnikoff’s theory.

The major causes of dysbiosis are:

• Dietary disturbances

  images High protein intake

  images High sugar intake

  images High fat intake

  images Low fiber intake

• Food allergies

• Lack of digestive secretions

• Stress

• Antibiotics or other drug therapy

• Decreased immune function

• Malabsorption

• Intestinal infection

• Altered pH

Obviously, treatment of dysbiosis begins with addressing these major causes.


Probiotics, which literally means “for life,” is a term used to refer to the health-promoting effects of “friendly” bacteria. The most important friendly bacteria are Lactobacillus acidophilus and Bifidobacterium bifidum. Because the intestinal flora play a major role in health, probiotic supplements can be used to promote overall good health. However, there are numerous specific uses for probiotics based upon clinical studies:

Benefits of Probiotic Supplementation Documented in Clinical Trials

• Promotion of proper intestinal environment

• Stimulation of gastrointestinal tract and systemic immunity

• Prevention and treatment of:

  images Antibiotic-induced diarrhea

  images Urinary tract infection

  images Vaginal yeast infections and bacterial vaginosis

  images Eczema

  images Food allergies

  images Cancer

  images Irritable bowel syndrome

  images Inflammatory bowel disease

  images Ulcerative colitis

  images Crohn’s disease

  images Traveler’s diarrhea

  images Lactose intolerance

Numerous analyses of commercially available probiotic supplements indicate there is a tremendous range of quality. The quality of probiotic supplements depends on the characteristics of the strains contained in the supplement and also on there being sufficient numbers of viable bacteria. Viability depends on a number of factors, such as proper manufacturing and the “hardiness” of the strain, as well as packaging and storage of the product at the correct temperature and humidity. Consumers should choose probiotics developed and manufactured by companies that have done the necessary research to ensure the viability of their products.

The dosage of probiotic supplements is based solely on the number of live organisms present in the product. Successful results are most often attained by taking between 5 billion and 20 billion viable bacteria per day.

Probiotics are very important in preventing the overgrowth of opportunistic organisms. For example, under normal circumstances the yeast Candida albicans lives in harmony with the host, but if the yeast overgrows and is out of balance with other gut microbes, it can result in problems.

In addition, probiotics help prevent parasitic infections. Most of the problems parasites cause involve interfering with digestion and/or damaging the intestinal lining, either of which can lead to diarrhea. Diarrheal diseases caused by parasites still constitute the greatest single worldwide cause of illness and death. The problem is magnified in underdeveloped countries with poor sanitation, but even in the United States diarrheal diseases are the third most frequent cause of sickness and death. Furthermore, the ease and frequency of worldwide travel and increased migration to the United States are resulting in growing numbers of parasitic infections in this country. These are discussed in greater detail in the chapter “Diarrhea.”

While the most commonly reported symptoms of parasitic infection are diarrhea and abdominal pain, these symptoms do not occur in every case. In fact, there appears to be a growing number of individuals who have parasitic infections but are experiencing milder than usual gastrointestinal symptoms and/or symptoms not traditionally considered to be linked to parasitic infections. For example, many cases of irritable bowel syndrome, indigestion, and poor digestion may be the result of parasitic infection. In addition, parasitic infections are often an unsuspected cause of chronic illness and fatigue.

Signs and Symptoms of Parasitic Infections

Abdominal pain and cramps


Depressed secretory IgA





Food allergy

Foul-smelling stools




Increased intestinal permeability


Irregular bowel movements

Irritable bowel syndrome

Loss of appetite

Low back pain


Weight loss

Detection of parasites involves collecting multiple stool samples at intervals of two to four days. The stool samples are analyzed by microscopy, specialized staining techniques, and fluorescent antibodies (the antibodies attach to any parasites and can be seen when they fluoresce).

There are a number of natural compounds that can be useful in helping the body get rid of parasites. However, before selecting a natural alternative to an antibiotic for treatment of parasitic infections, try to discern what factors may have been responsible for setting up the internal terrain for a parasitic infection. For example, do you have achlorhydria or decreased pancreatic enzyme output? Proper treatment with either an antibiotic or a natural alternative requires monitoring by repeating multiple stool samples two weeks after therapy. For more information on dealing with parasites, see the chapter “Diarrhea.”


An important way to help the probiotics become well established is to take prebiotics—basically, soluble fiber compounds that help feed the healthful bacteria. Traditional dietary sources of prebiotics include soybeans, inulin sources (such as Jerusalem artichoke, jicama, and chicory root), oats, and whole grains; supplements are also available. The typical dose is 3 to 5 g per day.

Lactose Intolerance

Lactose intolerance refers to the inability to properly digest lactose, the sugar found in milk and other dairy products. Most often lactose intolerance is due to a lack of lactase, an enzyme in the small intestine responsible for breaking the large molecule lactose into smaller, absorbable simple sugars. Lactose intolerance can lead to symptoms such as diarrhea, bloating, flatulence, and abdominal discomfort. Overall, lactose intolerance affects an estimated 25% of Americans and 75% of adults worldwide. However, the condition occurs more in some populations than in others. Many people with lactose intolerance are able to consume moderate amounts of lactose without symptoms, but in those with any symptoms avoidance of lactose or the use of lactose-reduced dairy products is a simple solution to lactose intolerance. Probiotic supplementation can often improve lactose tolerance.

Prevalence of Lactose Intolerance by Ethnic Group



African blacks




North American blacks




People of Mediterranean descent


People of Jewish descent


North American whites


Northern Europeans




• Indigestion can be attributed to a great many causes, including not only increased secretion of stomach acid but also decreased secretion of stomach acid and other digestive factors and enzymes.

• GERD is most often caused by overeating (reflux esophagitis) and impaired digestion.

• The natural approach to chronic indigestion focuses on aiding digestion rather than on blocking the digestive process with antacids.

• Common symptoms of pancreatic insufficiency include abdominal bloating and discomfort, gas, indigestion, and the passing of undigested food in the stool.

• Just as important as digestion is the elimination of waste from the body.

• Achieving and maintaining good colon health are straightforward: eat a high-fiber diet, drink plenty of water, and maintain health-promoting microflora.