by Dr. John Neustadt

A fundamental approach to health in naturopathic medicine is to “treat the gut.” Understanding how your gut works and that many symptoms that may not at first glance appear to have anything to do with your gastrointestinal tract, are in fact related. Taking a proactive approach by ensuring your gut is healed and is working optimally can help you feel better throughout your body.

Approximately 80% of all immune proteins are produced in the gut. The immune tissue in the gut is called Gut-Associated Lymph Tissue (GALT) and is the largest immune organ in the body.

This makes sense when you begin thinking functionally. What’s the role of the immune system? Very simply, it protects you from the outside world—bacteria, viruses, and parasites.

And what part of your body is most exposed to the outside world? Most people intuitively would say their skin, but in fact it’s your intestines (stomach, small, and large intestines). The intestines have a surface area that’s 3,229 to 4,306 square feet. That’s 20% of a football field! (An American football field has a surface area of 21,600 square feet.)

Technically the intestines are outside the body. They form a hollow tube from mouth to anus. When people put food or drink in their mouths, it doesn’t actually enter their bodies until it is absorbed through the cells lining the gut. The intestine’s exposure to the outside world and all of its dangerous microbes is inspiring.

Every day the average person consumes three to five pounds of food. That’s three to five pounds of the outside world being ingested. And every piece of food contains potentially millions of organisms, both harmful and beneficial. Even when someone eats optimally, he or she may not be digesting and assimilating the nutrients properly.

There are three major reasons for this: digestion may not be functioning properly due to chronic stress; food intolerances may be causing chronic immune activation in the gut; or intestinal bacterial, fungal, or protozoal infections, called intestinal dysbiosis, may be causing inflammation and decreased digestion.

Each of these situations can occur individually or together, placing one at risk for decreased ability to digest and absorb nutrients.

Healthy Digestion

Digestion involves the breakdown of large molecules into smaller, readily absorbed molecules. Whereas some digestion begins with the production of enzymes in the mouth, the stomach is where the process of digestion really takes place.

Cells in the stomach excrete specific enzymes to break apart fats, starches, and proteins. The enzymes, however, are inactive and must be activated by stomach acid. When someone produces enough stomach acid, proper digestion in the stomach occurs. But many people don’t produce enough stomach acid.

Low stomach acid production is called hypochlorhydria, and when no stomach acid is produced, it’s called achlorhydria. Decreased stomach acid production occurs from aging, caffeine, overeating, stress, medications (especially those that block the production or excretion of stomach acid such as Protonix, Tagamet, Pepcid, Axid, Zantac, Prevacid, Prilosec, Aciphex, and Nexium), alcohol, and stomach surgeries that destroy the acid-producing cells.

Many people produce less stomach acid as they age. It’s been estimated that 10–21% of people sixty to sixty-nine years old, 31% of those seventy to seventy-nine years old, and 37% of those above the age of eighty have hypochlorhydria or achlorhydria, and this rate may be higher in people with autoimmune conditions.

One question posed to patients to screen for their risk of low stomach acid is, “Do you feel fuller sooner than you used to and stay full longer than you used to when you eat?” If the answer is yes, it may be that they have low stomach acid, since decreased stomach acid increases the amount of time food sits in the stomach before passing into the small intestines.

When stomach acid is low, vitamins and minerals may not be efficiently released from the food that contains them. This may result in decreased availability of nutrients for absorption and nutritional deficiencies. People with low stomach acid have been shown to be at increased risk for vitamin and mineral deficiencies.

Symptoms of low stomach acid production include bloating or distension after eating, diarrhea or constipation, flatulence after a meal, hair loss in women, heartburn, indigestion, malaise, and a prolonged sense of fullness after eating.

Additionally, the risk of hip fracture increases by 22% after one year and nearly 60% after four years in people taking proton-pump inhibitor (e.g., Protonix, Prilosec, Nexium, Aciphex) and H2-receptor antagonist (H2-blockers; e.g., Cimetidine and Ranitidine (Zantac)) medications compared to people not taking them.

Stomach acid plays two other important roles. It acts to sterilize food and signals the lower esophageal sphincter (the muscle separating the esophagus from the stomach) to close. When low stomach acid production decreases the ability of the lower esophageal sphincter to close, the result is that the acid produced in the stomach can reflux up into the esophagus and cause symptoms of GERD.

The typical medical response to gastric reflux, which can cause burning, coughing, and asthma-like symptoms, is to prescribe acid-blocking medications. However, the actual cause in many people is too little acid and not too much acid.

Decreased acid production can occur as a result of decreased histidine, an amino acid that is required for acid secretion. This amino acid is tested as part of an amino acid blood panel, which may diagnose the underlying cause in some patients. Providing histidine to people with low stomach acid may improve their stomach acid production.

Stomach acid production can also be tested by using a meter, called a Heidelburg pH capsule test.

Low stomach acid can also occur in from infections, such as Helicobacter pylori (H. pylori) in the stomach. Additionally, when people have low stomach acid production, some doctors provide hydrochloric acid capsules for people to take with meals that help improve their digestion and eliminate GERD.

There are some instances when people should not supplement with acid pills, and I advise people against supplementing with hydrochloric acid unless under the care of a doctor.

Healthy Gut Microbes

The gut normally contains about four hundred different species of bacteria, which are required for normal digestion and absorption of nutrients. It has been estimated that there are more bacterial cells in the gut than all the cells in the body combined. Not only are these beneficial bacteria required for normal digestion and absorption of nutrients, the probiotics make nutrients for you.

When inadequate sterilization of food occurs, however, pathogenic bacteria, viruses, and fungi can pass into the small intestines. This disrupts the healthy ecology in the gut and alters the delicate balance between healthy and unhealthy microbes.

It is now recognized that gut immunity plays a central role in systemic health. For example, it has been observed that gastric acid suppression, using H₂-blockers and proton pump inhibitors is associated with an increased risk of community-acquired pneumonia.

It is suspected that acid suppression results in insufficient elimination of pathogenic organisms. It has therefore been suggested that patients at higher risk of pneumonia should only be prescribed proton pump inhibitors at lower doses and only when necessary.

Dysbiosis can occur with the overgrowth of pathogenic bacteria, parasites and/or fungi. Symptoms of intestinal dysbiosis include abdominal gas and bloating, post-nasal drip, “brain fog” (feeling like you’re just not mentally sharp), and sugar cravings. Abdominal gas and bloating are caused by fermentation of food by microorganisms, which produce methane.

Post-nasal drip is caused by immune system activation in the gut. GALT activation stimulates histamine release, which increases vascular permeability and causes symptoms of rhinitis or post-nasal drip.

Sugar is the preferred energy source for the fungi, which can lead to sugar cravings. Bacteria and fungi secrete their own waste products, such as ammonia, that can enter the blood stream, cross into the brain, and cause brain fog. Additionally, intestinal bacterial overgrowth is now understood to be a risk factor for developing gastroesophageal reflux disorder (GERD).

The new generation of stool tests is the most sensitive and specific at detecting gut pathogens. Normally when physicians suspect a parasitic infection an ova & parasite (O&Px3) test is ordered. In an O&Px3 test, a patient provides samples of his or her stool that are evaluated under a microscope by a parasitologist who is literally looking for small parasite eggs or the mature parasites themselves.

To detect a parasite the parasitologist must rely not just on his or her skills, but also on luck. The parasitologist must be lucky enough to have a stool sample by chance that had a large enough parasite or egg in it to be seen through a microscope. They do not look at every square centimeter of the stool but take samples from the stool to look at. They therefore must also be lucky that the random sample they took had something in it. This test is highly unreliable.

The most advanced testing analyzes stool samples for parasite DNA fragments. Instead, the stool sample is run through a sophisticated machine. The stool sample does not need to have an intact parasite or egg in it. This eliminates the role of luck in the process. Instead, the stool sample is run through a sophisticated machine and only five cells from an organism are required to detect it.

Common parasite infections diagnosed by this technology include hookworm (Necator americanus), whipworm (Trichuris sp.), and Cryptosporidium sp. Additionally, from this one stool sample the tests can detect H. pylori infection in the stomach, bacterial and yeast infections in the intestines, and if your intestines are low in healthy bacteria.

H. pylori is a bacterium that colonizes the stomach and is considered a Type I carcinogen. Most physicians will not test for any of these other infections, even though the symptoms significantly overlap with a parasite.

Parasitic diagnoses are very rare because most physicians are not trained in parasitology. It’s the rare medical school that will expose its students to a six- or eight-week course in parasitology. Most standard medical evaluations do not include a parasite test, and even when they do it’s an extremely insensitive test. Why might it be important to test for parasites? Because the symptoms mimic many other diseases.

Healthy Foods

While the healthiest eating pattern is a whole foods diet that limits processed and fried foods, if you’re having allergic reactions to foods you’re eating you can still be damaging your intestines. Food intolerances can cause decreased absorption of nutrients by creating chronic inflammation in the intestines.

Eighty percent of the immune system is clustered around the intestines. When people repeatedly consume food that causes an immune activation in the gut, it creates intestinal irritation. Over time, the cells lining the intestines become damaged. This can create malabsorption with decreased ability to assimilate nutrients from food.

An extreme example of this is Celiac disease. Intolerance to wheat, rye, barley, and oats characterizes this disease. The immune system actually reacts to gluten contained in these foods. This causes intestinal inflammation and destruction of the cells lining the intestines. Celiac disease has wide-ranging symptoms, including fatigue, anemia, joint pains, depression, loss of balance, and malnutrition.

More frequently, people will react to foods that they crave, such as milk and eggs, which can be detected through a special blood test. This blood test is called an IgG food intolerance test, and people with rheumatoid arthritis, eczema, and other conditions have been shown to have elevated IgG antibodies to foods. IgG is a protein produced by the immune system.

Most doctors only test for IgE-mediated allergies, which are also called “immediate hypersensitivity reactions.” An IgE-mediated-immune response is responsible for the life-threatening reaction in some people to bee stings or peanuts. IgG, on the other hand, is a delayed-type-hypersensitivity reaction that, as the name implies, is not immediately apparent. People who test negative on an IgE test can be positive on an IgG test.

IgG reactions may take hours or days to appear, and symptoms can include post-nasal drip, gas and bloating, difficulty losing weight, joint aches, eczema, fatigue, and others. Food intolerances can cause these diverse symptoms for various reasons. Similar to bacterial and fungal dysbiosis, the immune-system activation caused by food intolerances can cause post-nasal drip.

Gas and bloating is a result of incomplete digestion of food and the resultant fermentation of these food particles by microorganisms in the intestines. Difficulty losing weight may result from an increased cortisol response by the body due to the continual stress placed on the immune system. When cortisol is chronically elevated, it causes an accumulation of abdominal fat.

The explanation for eczema and joint pains is a little more complicated. When the immune system in the intestines is activated, the antibody-antigen complexes enter the blood stream. An antibody is the protein produced by the immune system such as IgG, and an antigen is the molecule against which the immune system is reacting, such as a protein in milk.

These antibody-antigen complexes travel from the intestines to the liver, where they are broken down for elimination by the body. This process is like a conveyor belt where the antibody-antigen complexes are delivered to the liver for processing, but the amount of complexes delivered to the liver over time can overwhelm the liver’s ability to detoxify them. When this occurs, the complexes pass through the liver and enter the systemic circulation.

Like bits of sand in a river, these complexes can settle out of the blood stream where the flow of blood slows down. This occurs in the skin and joints. When these complexes are deposited in skin and joints, they act as irritants that can create local immune-system activation and produce such symptoms as joint pains and eczema. Frequently, the joint pains will be migratory, meaning different joints will be affected at different times.

Chronic stress destroys collagen, predisposes people to low stomach acid production and food intolerances. This is because stress stimulates the release of cortisol, norepinephrine, and epinephrine. These are part of the flight or flight response to stress. The analogy that’s often used to teach this concept to medical student is, “Imagine that you’re being chased by a tiger.” The body has two responses. It either flees or battles it out. In either case, cortisol and epinephrine are secreted to prepare people for action.

They increase blood flow to skeletal muscles and decrease it to the intestines. These hormones also increase heart rate and alter blood flow in the brain. By shifting blood flow away from the intestines and to the muscles, digestion decreases. This can also cause damage to the cells lining the intestines and create a “hyperpermeable gut.”

When digestion decreases, it allows larger food particles to enter the small intestines, where food is absorbed through the lining of the gut and into the body. The larger food particles, combined with the damaged lining of the gut, can activate the immune system and create food intolerances. As you might be gathering, many health complaints are directly related to and caused by an unhealthy intestinal tract.

Identifying any food allergies and intestinal infections are crucial to healing the gut. The goal is remove the things (e.g., aggravating foods and infections) that are causing the problems and then initiate a gut repair protocol using specific nutrients to make the gut healthy.

One key nutrient is L-Glutamine, an amino acid that is an energy source for cells in your digestive tract. This provides nutrition to the gut to help the cells heal. Herbs that soothe the gut are also sometimes used. The ability of the body to break down toxins and eliminate them in the urine and stool is a vital determinant for overall health.

While as much as 75% of detoxification activity occurs in the liver, much of the remainder takes place in the intestinal mucosa wall. Still, an additional small percentage occurs in other tissues. Although we usually think of the liver as the detoxification site, it makes sense that the intestine also plays an important role in detoxification, since the gastrointestinal lining provides the initial physical barrier to the largest load of xenobiotics (substances from outside the body), including orally ingested drugs.

The GI tract also influences detoxification by hosting gut microflora capable of producing compounds that may either induce or inhibit detoxification. Although the liver and intestinal mucosa contain the majority of the detoxification enzymes, the importance of detoxification explains the occurrence to some degree of detoxification activity in all cells.

A healthy gut is required for creating optimal health. It’s important to ensure you’re eating the best foods and exercising (here are 5 Simple Ways to Work Exercise into Your Life) but it’s also vitally important to repair any gut damage.

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