Gut Health: The Key To a Healthy Life

Modern medicine is learning what many traditional cultures knew all along—a  healthy gut is critical for a healthy body.

There are two principal reasons for this—nutrients and immune health. Without the ability to process and assimilate key nutrients into the body, everything from brain function to muscle integrity suffers. A healthy gut digests everything we take in and grants access to these vital nutrients, which impact every cell in the body. Less obvious but equally critical is the role the gut plays in regulating the immune system and identifying friend from foe.

The digestive process is a bit of a mystery to most people. We know what goes in and what comes out—it’s what happens in between that turns everything from leaves of lettuce to bites of meat into fuel and essential building blocks for our bodies where many of us lack some details. The digestive system has five main functions: (1) breaking down food into usable nutrients; (2) absorbing nutrients; (3) keeping out invaders and identifying friend from foe; (4) regulating the immune system; and (5) eliminating waste.

Modern medicine is learning what many traditional cultures knew all along—a  healthy gut is critical for a healthy body.

The process begins in the mouth with chewing, an under-appreciated part of digestion, which breaks food down into smaller pieces that would otherwise have to be broken down by chemical processes alone. Chewing also moistens and mixes the food with saliva. The first chemical breakdown of food also occurs in the mouth thanks to salivary amylase, an enzyme that begins breaking down carbohydrates. Afterwards, food in the mouth is swallowed and travels down the esophagus to the stomach.

The body requires both macro and micronutrients. There are three main types of macronutrients—carbohydrates, fats and proteins. “Carbs” come in simple forms such as sugars as well as complex forms, which are basically chains of sugars. Foods like rice, bread, potatoes and pasta are rapidly broken down to sugar and tend to spike blood sugar levels relatively quickly. Foods with more complex forms of carbohydrates, including most vegetables, are broken down more slowly and tend not to raise blood sugar very much. Still other carbohydrates cannot be broken down by our body and may pass through the upper part of the digestive system and into the colon, where they serve as food and fuel for the microbes living there.

The other two main macronutrients also serve key functions. A substantial portion of the human body consists of protein, and amino acids serve as the building blocks of protein to enhance our bodily functions and make muscle. Fats are equally important. They are the most dense source of calories for the body, yielding 9 calories/gram compared to 4 calories/gram for protein and carbohydrates; they serve as reservoirs of energy storage for the body and as the key components of our cell membranes. They are also critical for maintaining cell structural integrity.

A Healthy Gut

Once food reaches the stomach, it’s mixed with fluids and stomach acid. Stomach acid is in actuality hydrochloric acid, a strong chemical acid, but thanks to mucus and a specialized lining, the stomach remains protected, enabling it to serve as a holding tank that regulates the delivery of food to the intestines. Acid is vitally important to the breakdown of food, especially proteins, which are broken into smaller fragments that can be further digested in the intestines.

Two other vital organs that feed into the upper intestines and perform critical digestive functions are the liver and the pancreas. As the metabolic powerhouse of the body, the liver produces many important proteins and detoxifies chemicals and hormones and excretes them into the bile. Bile is concentrated in the gallbladder, which pumps it into the intestine when stimulated by food. Bile allows the liver to rid the body of toxins and metabolic waste products and helps with the digestion of fats through emulsification, making them more soluble.

The pancreas plays a central role in both digestion and regulating metabolism through the production and secretion of insulin, along with other hormone-like molecules. The pancreatic fluids secreted into the intestines contain three different types of digestive enzymes—proteases, lipases and amylases. Proteases break down protein into smaller pieces and eventually into amino acids. Lipases break down fats into fatty acids and amylase breaks down starch into sugars. As such, it’s easy to assess the importance of digestive enzymes. However, disease and the aging process can limit production. When this happens, it can prove beneficial to add enzyme supplements to your diet on a regular basis.

Food from the stomach is fed into the small intestine, where the majority of nutrients are absorbed. It consists of three parts—in digestive order the duodenum, the jejunum and the ileum. The small intestines have many folds and are covered with multiple projections, called villi, which in turn are covered with microvilli that further increase the surface area to over 400 square feet.

Adequate breakdown of food and the health and integrity of the intestinal lining are both key to preserving health. In a healthy gut the lining is protected by intact membranes that form a tight seal to keep anything from seeping between the cells into the bloodstream. But a damaged or leaky lining allows protein fragments and other molecules that would normally remain in the gut to pass through and enter the bloodstream. And if the proteins, carbohydrates and fats are not fully broken down by stomach acid and enzymes before entering the bloodstream, the situation becomes even worse.

When digestion is incomplete due to a lack of stomach acid, deficiencies in digestive enzymes and insufficient bile or a microbiome that is out of balance, larger particles may get into the bloodstream.

Once these larger molecules that normally stay inside the gut reach the bloodstream, the immune system identifies them as foreign invaders and attacks by targeting antibodies and different types of immune cells against them. When the problem of incomplete digestion causes symptoms in the gastrointestinal (GI) tract itself, bloating, diarrhea, constipation or abdominal pain may occur.  And when these fragments travel throughout the bloodstream, autoimmune problems such as certain types of arthritis or even thyroid problem issues occur.

Where  Do Healthy  Bacteria In The Gut  Come From?

Babies are born without any bacteria in their gut; those born vaginally develop a wider variety of healthy normal bacteria sooner than babies born by Cesarean Section as the trip through the birth canal inoculates them with healthy bacteria from the mother. While the full adult microbiome does not usually get established until around age 4, children who  have siblings, grow up with a dog, go to daycare and play outdoors are less likely to have certain types of health  problems (such as asthma) and tend to have more  complete and healthier microbiomes.

What Can Go Wrong?

Troubles with the GI system can occur anywhere along the way. Dry mouth and insufficient chewing can lead to swallowing problems, as well as issues breaking down food, since the body depends on the mechanical crushing action of chewing to increase the surface area of food and, in turn, to give the stomach acid, bile and enzymes a chance to act on that food.

If you have eaten a wide variety of live foods throughout your life and rarely if ever taken antibiotics, you may have a diverse and healthy population of bacteria in your system. However, the diversity of the microbiome may decrease as you age, leading to the theory that this may be an important factor in the development of different diseases and a loss of resilience with age. If you have taken antibiotics during your life, your gut bacteria may be even less complete. In these circumstances taking a probiotic supplement on a regular basis may enhance your overall health.

GERD – Acid Reflux


Food passes from the esophagus into the stomach through the LES (Lower Esophageal Sphincter) which acts like a valve, letting food into the stomach and preventing it from reentering the esophagus. However, when the LES fails to do its job, acid from the stomach or bile can back up into the esophagus, damaging the esophageal tissue and potentially causing burning pain or scarring.

Reversible factors that can cause or worsen Gerd:

  • Caffeine
  • Tobacco
  • Alcohol
  • Mint or Peppermint
  • Obesity
  • Certain Medications

Stomach Problems

Stomach problems stem from three main causes: infections with the bacteria Helicobacter pylori, medications and substances that damage the lining of the stomach and form substances that increase stomach acid. Mild to moderate stomach problems result in gastritis, damage to the surface of the stomach lining, while more serious problems result in ulceration. Stomach ulcers can form deep holes in the stomach lining and cause serious bleeding or even perforation. Helicobacter pylori infections can be identified with blood, stool or breath tests. The infection can be eliminated with a combination of antibiotics and other stomach medicines. Treating Helicobacter infections greatly increases the chance of healing the ulcer and helps to prevent recurrence.

Factors That Cause Stomach Ulcers:

Agent: Helicobacter Pylori Infection
Mechanism: Infiltrates stomach lining

Agent: Aspirin/NSAID Medications
Mechanism: Directly damage stomach lining

Agent: Alcohol
Mechanism: Directly damage stomach lining

Agent: Caffeine
Mechanism: Increase stomach acid output

Agent: Tobacco
Mechanism: Increase stomach acid output

Achlorhydria – Problems With Too Little Stomach Acid

Insufficient stomach acid can also cause problems. Stomach acid helps break down food and to form a first line of defense against many organisms we ingest. Insufficient stomach acid, known as achlorhydria, not only results in poor digestion; it is also associated with lower absorption rates of certain nutrients such as calcium and with a condition called Pernicious Anemia, which occurs when intrinsic factor, an element produced in the stomach essential for the absorption of Vitamin B-12 production, is not made. This results in a severe Vitamin B-12 deficiency that can cause anemia, nerve damage and even cognitive decline.

Intestinal Problems

Digestion difficulties in the intestines can involve the small or the large bowel. The large bowel is called the colon. Celiac Disease is an autoimmune disorder involving the destruction of the lining of the first portion of the small bowel, which results from a reaction to gluten. In Celiac and many diseases that affect the bowel, the villi and microvilli are destroyed, leading to a loss of the ability to absorb nutrients. When this happens a variety of secondary problems can occur throughout the body due to a lack of these nutrients.

A healthy population of bacteria in the intestines is also critical for digestion, as these bacteria produce substances that nourish the cells that line the gut along with certain vitamins and other nutrients. If your microbiome (the organisms within your gut) is out of balance or declines in quality with age, probiotic supplements can be of value. In addition to a healthy population of bacteria, it’s also vital to have the right food to fuel them. Certain fibers can serve as prebiotics to fulfill this function. However, if your diet is lacking in healthy fibers, taking prebiotic supplements along with probiotics may improve the health and quality of your microbiome.

One of the most common bowel conditions is irritable bowel syndrome (IBS), which can cause pain, diarrhea and constipation. Stress plays a significant role in the communication between the nervous system and the bowel, and disorders such as IBS may improve with effective stress management techniques. Inflammatory bowel diseases (IBD) are more serious bowel disorders that can result in damage to the lining of large sections of the intestines and can lead to serious bleeding, obstruction and perforation. Diseases such as Crohn’s Disease and Ulcerative Colitis are inflammatory bowel diseases.

Functional Medicine Approach to Health the Gut

Functional Medicine uses an approach called 5R to heal the gut. 5R stands for:

Remove, Replace, Repopulate, Repair and Rebalance.

Different versions of this approach can be used to treat a variety of problems throughout the gut. Functional Medicine practitioners believe that treating gut problems is a critical element in healing not only GI problems  but also a wide variety of problems throughout the body.


Removing refers to eliminating both pathogenic organisms such as parasites or excessive yeast as well as medicines or chemicals that damage either the gut itself or the health of the gut bacteria—the microbiome. Removing toxic chemicals and medicines primarily involves avoiding them to the extent possible. Sometimes special programs or supplements are used to help the body eliminate toxins.


Replace in the 5R treatment approach refers to replacing elements that may be missing such as stomach acid or digestive enzymes. It could also include replacing important elements missing in the diet such as vegetables or grains, which include prebiotic fibers that nourish and serve as food to maintain a healthy and diverse microbiome. If you aren’t getting enough beneficial  ingredients from dietary sources, taking a prebiotic supplement  may be of value.


Repopulate refers to reseeding the gut with healthy microbes.  In the early 1900s, pioneering researcher Eli Metchnikoff puzzled over why certain people in the mountains of Bulgaria lived considerably longer than others. He found that these healthy mountain villagers were regularly drinking fermented yogurt, which contained a probiotic species that was a type of Lactobacillus. It clearly seemed to improve their health and also may have extended their lives. Based on Metchnikoff’s work, over the years others have done further work to enhance understanding. Modern research has shown that different beneficial bacteria have different positive effects in the body. These range from improving the symptoms of irritable bowel syndrome to lowering cholesterol and anxiety. These can come in foods like fermented yogurt, live foods such as sauerkraut and kimchee or from specific probiotic supplements. The most effective way to change the population of microbes in the colon is fecal microbial transplant [FMT], or stool transplant. When successful, this seems to result in a more significant and sustainable change in the microbial population. Fecal transplant is most commonly used for patients who have recurrent life-threatening colon infections with the bacteria Clostridium difficile, although a number of other conditions may also benefit. 

Foods that may have prebiotic effects:

Asparagus, garlic, leeks, legumes, oats, sea weed, onion, bananas, dandelion greens, barley, wheat bran, Jicama root, Jerusalem artichokes and artichokes.


The Repair in the 5R approach refers to supplying important nutrients that help to improve the health of the cells lining the gut. This includes giving substances that can sustain and nourish the cells that line the stomach and intestines such as the amino acid glutamine as well as micronutrients like zinc, along with a spectrum of vitamins.  When the stage has been set by removing harmful elements and repopulating the gut with healthy microbes, these healthy substances can help heal the lining of the intestines and make it less likely to be a leaky gut. This in turn can lead to improvements in health throughout the body.


Rebalance is the final phase of improving gut health. If the body is under sustained chronic stress, cortisol and other hormones change the environment in the bowel. This makes it more favorable for the unhealthy bacteria and less favorable for healthy species of bacteria and other microbes. Stress management, counseling and mind-body work such as MBSR (Mindfulness Based Stress Reduction), T’ai Chi and Yoga can help rebalance the autonomic nervous system and allow the body to develop a healthier level of gastrointestinal function.

5R Gut Healing Table – Examples


Agents to Change:
Remove gluten in Celiac Disease and other sensitive individuals; remove harmful parasites, excessive yeast and harmful bacteria species; remove toxic chemicals and unhelpful medications


Agents to Change:
Stomach acid replacement; digestive enzyme replacement; bile salt replacement when deficient; providing prebiotic fiber

Products and Approaches of Value:
Digestive enzyme supplements; prebiotic dietary fibers; prebiotic supplements


Agents to Change:
Replace healthy microbes

Products and Approaches of Value:
Live foods such as live culture yogurt and sauerkraut; probiotic supplements


Agents to Change:
Provide essential compounds for the health of gut cells

Products and Approaches of Value:


Agents to Change:
Stress reduction techniques

Products and Approaches of Value:
T’ai Chi program; healing prayer


Understanding that gut health is a key factor in your overall health is an important step. It also helps to unravel numerous issues that arise at different stages of digestion. By understanding each step and what can go wrong, we can take measures to preserve and restore the health of the entire GI system. A Functional Medicine approach relies on a deep understanding of what promotes health and what it takes to nourish and heal the gut to promote system wide health. The combination of a healthy gut and a healthy diet can allow us to optimize our nutrition, which can contribute to optimal health in tissues throughout the body. While it’s obvious that gut health relates to issues of the digestive organs, less obvious but equally important is understanding the role a healthy gut plays in issues as diverse as the regulation of the immune system and the health of the brain.

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About Robert Sheeler, M.D. 

Robert Sheeler, M.D.

Dr. Robert Sheeler is a Family Physician who spent a substantial part of his career at Mayo Clinic. During that time he served as the Medical Editor for the Mayo Clinic Health Letter, taught and developed curriculum in the medical school and chaired the NeuroPsychiatric Medicine group. In addition to Family Medicine, he is also certified in Functional Medicine through the Institute for Functional Medicine and as a sub-specialist in Headache Medicine through the United Council of Neurologic Sub-specialists. Dr. Sheeler is Board Certified in Urgent Care, Holistic-Integrative Medicine and Integrative Medicine as well. He has strong interests in nutrition, cooking, stress management and lifestyle medicine and also practices and teaches Taiji [T’ai Chi] and Qigong. 


I believe that a balanced lifestyle and a diet rich in healthy anti-inflammatory natural foods can be of significant value in preserving and restoring health. Natural products often make more sense than pharmaceuticals, as they seem to alter biochemical pathways more gently rather than turning off whole systems our body naturally utilize.

A diet that contains diverse types of vegetables along with some fruits is often best to promote a diverse and healthy population of gut microorganisms. I try to eat 2 servings of fruit a day—usually fruits that do not raise blood sugar as much such as berries and apples and 5 servings of different types of vegetables a day along with healthy proteins and healthy types of fats such as olive oil, especially EVOO, avocado oil and coconut oil.

Beyond eating right, exercising and getting adequate sleep, I believe that meaningful relationships, community and spiritual connection are also of great value.