If you eat a typical Standard American Diet (SAD) comprised of mostly white and brown colorless and processed foods and you have been suffering from fatigue, joint pain, anxiety, depression, irritable bowel syndrome, heartburn, weight gain, bloating, gas, chronic pancreatitis, ulcerative colitis, or Crohn’s disease, you’ll want to implement aspects of the Five ‘R’ Approach to gut health.

The gastrointestinal system (or the gut) is the core system to initiate either healing or disease in a multi-systems approach to human health.


These five actions are Remove, Replace, Re-inoculate, Repair, and Rebalance.

First and foremost, we must remove the processed, packaged, irradiated, and sugar-laden foods from our everyday intake. Next, remove foods that cause irritation and inflammation to our immune system. Foods that trigger an immune response may differ from person to person but completing a Comprehensive Elimination Diet can determine what foods are wreaking havoc in your immune system. The categories that are typically linked with an immune response include gluten, dairy, eggs, soy, alcohol, processed foods, sugar, caffeine, peanuts, and shellfish.

We live in a symbiotic relationship with bacteria and would die without bacteria in our colon. But, as much as we want the good bacteria to reside in our gut, we want to remove bad bacteria. There are many forms of bacteria and yeast, like candida, that can cause dysbiosis or dis-ease in our gut environment. A comprehensive stool analysis can report which bacteria are present in your stool and to what quantity or degree. If needed, different treatments such as antibiotics, antimicrobials, herbs, supplements, and dietary changes can be taken to remove the bad bacteria and promote the good bacteria.

Finally, remove all medications* that may be promoting an unhealthy environment in your gut. Anti-inflammatory medications like ibuprofen or other NSAID’s can promote intestinal permeability, or leaky gut, and should be removed or limited as much as possible. Antacids are not meant to be taken for long periods of time as the stomach is supposed to be an acidic environment with a pH around 2. Altering the pH of the stomach prevents contents of the digestive tract to regurgitate back up the esophagus and cause heartburn or gastroesophageal reflux disease (GERD).


If our digestive tract and the organs that support it are not functioning optimally, then there are supplements and foods that you can take to replace the different enzymes and other chemicals necessary.

Digestion is the process of breaking a bite of food down into the nutrients we absorb (protein, carbohydrate, and fat molecules). The process of digestion begins in the mouth with chewing and an enzyme in our saliva called amylase. This enzyme starts the process of breaking down carbohydrates. Swallowing then sends the food down the esophagus to the stomach.

The stomach is an acidic environment (pH of 1.5 – 3.0) filled with hydrochloric acid (HCl), which kills bacteria in our food, and pepsin, which breaks down proteins into individual amino acids. These amino acids need to be broken apart in the stomach and upper intestine in preparation for absorption in the lower intestine.

Ensure that you are chewing food thoroughly before swallowing and optimizing your stomach acid. Things that can be taken to optimize stomach acid are apple cider vinegar and/or lemon juice diluted in a small glass of water and consumed prior to meals.

Supplements of betaine HCl and pepsin enzyme can be taken with meals to help increase stomach acid and improve stomach digestive function in those without ulcers or severe heartburn. Those with ulcers or severe heartburn should work with a functional medicine practitioner to improve the situation with food and diet and other measures prior to adding HCl supplements.

The pancreas produces a collection of pancreatic enzymes that can break down fats, carbohydrates, and proteins and secretes these enzymes into the upper small intestine. Many people with gut problems and dysbiosis are not breaking down the foods they eat effectively and need to replace or supplement pancreatic enzymes with meals.

The gallbladder produces and secretes bile salts into the intestine to help breakdown fats and remove cholesterol and toxins. These bile salts also help with the motility or movement of digested substances through the digestive tract. Bile salts can be taken as a supplement such as ox bile, but eating certain foods like dandelion greens, chicory, artichokes, and daikon radishes can increase the production of bile salts as well.


The human colon is populated with as much as two pounds of bacteria and outnumber human cells by a ratio of 10:1. We must promote diversity and stability of the beneficial gut bacteria with probiotics and prebiotics. The beneficial bacteria in the colon have numerous functions that include helping with fermentation and digestion, providing protection against pathogens, synthesizing vitamins, and producing short-chain fatty acids.

Probiotics are dosed in billions of CFU’s. This stands for “colony forming unit” and is a measurement of the good bacteria and yeasts capable of living and reproducing to form a group of the same bacteria or yeasts.

When first initiating re-inoculation to optimize gut health, a higher dose of probiotics (100 billion CFUs) are taken daily. Later, a more maintenance dose of 10 to 20 billion CFUs daily can be used. More and more studies are showing that diversity is the most important aspect of a healthy gut microbiome, so eating probiotic foods daily is extremely important.  Probiotic foods include yogurt, miso, sauerkraut, kefir, kombucha, pickles, tempeh, and kimchi.

Prebiotics are typically water-soluble fiber that is not digestible by the host (human) enzymes and therefore get fermented and digested by anaerobic bacteria in the colon. The product of this fermenting by the bacteria in your gut are short chain fatty acids that are used as fuel by the enterocytes (cells lining the gut). If you want a healthy gut lining, then you need to be ingesting good prebiotics every day. Supplemental prebiotics include inulin, fructooligosaccharides, and arabinogalactans, while food source prebiotics include onion, garlic, Jerusalem artichokes, leeks, chicory, chia seeds, flax seeds, asparagus, bananas, root vegetables, and apples.


The epithelial cells that line our gut are only one cell layer thick. The connections or junctions between these cells are supposed to be very tight so that this lining acts as a barrier. Only small nutrient molecules of protein, fat, carbohydrate, vitamins, and minerals are to be absorbed. If these tight junctions loosen and gaps are formed, this can cause significant problems because it allows larger particles to be absorbed through increased intestinal permeability or “leaky gut.”

There is also a mucus layer in the intestines and colon that protects the epithelial cells, keeps the cells hydrated, and helps the contents of the intestine move through the digestive tract so that nutrients are absorbed but waste is expelled.

To optimize gut health, you’ll have to repair the gut lining and mucus layer. Some of the most common supplements and foods used to repair the gut lining and mucus layer include:

  • L-glutamine – an amino acid, a building block of protein
  • Bone broth – broth made from chicken or beef bones
  • Prebiotic foods – water-soluble fiber that becomes fermented and digested by anaerobic bacteria in the colon
  • Slippery elm – supplement derived from the inner bark of a species of elm tree


The gastrointestinal or enteric nervous system is embedded in the lining of the gastrointestinal system, beginning in the esophagus and extending down to the anus.

The enteric nervous system has been described as a “second brain” and can operate autonomously or separately from the rest of the body’s nervous system.

The nerves of the gastrointestinal nervous system control peristalsis, the contractions of the intestinal muscles that churn and move digested food through our gastrointestinal tract. The enteric nervous system is also responsible for the secretion of several different enzymes, proteins involved in digestion and other chemical reactions.

The enteric nervous system also makes use of more than 30 neurotransmitters, most of which are identical to the ones found in the brain, such as acetylcholine, dopamine, and serotonin. These neurotransmitters can be very involved in mood stability, anxiety, and depression so maintaining neurological and psychological balance is extremely important when it comes to your gut health.

The chronic stress that modern life imposes on us can take an enormous toll on our health and well-being if we do not rebalance our nervous system.

One of the best ways to balance your cortisol or stress hormone levels is to get at least 8 hours of sleep per night. Trouble falling asleep or waking in the middle of the night and have trouble getting back to sleep are both signs of cortisol imbalances. Taking a low dose of melatonin (3 mg) prior to bedtime can be very helpful not only for sleep but also for quieting the enteric nervous system in people with multiple gut problems such as heartburn and irritable bowel syndrome.

Another way to rebalance your nervous system is to have a daily stress reduction practice. Breathing exercises, for example, can be done in many different mindful ways to quiet the mind, reduce stress, and improve oxygenation. Meditating can involve emptying the mind of all thought or giving the mind something to focus on mindfully, such as repeating a mantra or prayer. Activities like yoga, walking in nature, or dancing can all be forms of moving meditation.  Practicing any or all these stress-reducing activities daily will help to rebalance your nervous system.

For more support and guidance about implementing the Five ‘R’ Approach, please schedule your free phone consultation to speak with a staff member from Discover Health Functional Medicine Center.

* Please note that the functional medicine approach to healing the gut does not happen overnight and it is never recommended that a person should remove any medication right away.