Good Health Starts in the Gut

We don’t generally pay much attention to our digestive processes, unless something goes wrong, of course. But the process of eat­ing, breaking down the food, and then ab­sorbing it is truly an amazing process. Each time we eat, our food begins the long jour­ney that will progressively break it down into its most basic parts so nutrients can be absorbed and unusable parts can be excret­ed. The digestive system is also responsible for defending the body against foreign in­vaders, removing bodily wastes, destroying old intestinal cells and creating new ones, fostering the growth of beneficial bacteria, making certain vitamins like K and B12, and releasing hormones that communicate with the brain and heart. Without this complex system, we wouldn’t get the nutri­ents we need to constantly fuel bodily processes. The problem is that this intricate system is eas­ily derailed by our modern lives. Stress, chemicals and pesticides, a lack of fiber, and the use of medi­cations can all alter the functioning of the gastro­intestinal system and the beneficial bacteria that reside there. Once the gut becomes compromised, the whole body suffers.

The symptoms that indicate a need for gut healing are numerous but may include gas, bloating, cramping, food allergies and sensitivities, indigestion, leaky gut, or skin conditions like acne and eczema. Stool appearance (including shape and color) and daily number of bowel movements are other good indicators of gut health. Stools that are separate, hard and lumpy (constipation) or liquid and mushy (diarrhea) or that are off in color (ex: yellow or black) are signs that your digestion is suffering. Normal, healthy stools are well-formed, easy to pass, smooth and soft, and brown in color. An ideal frequency is 1-3 times per day with the absence of straining and no sign of undigested foods. Going less or more than this indicates that your digestion needs some work.

While fiber is important for the health and regularity of the digestive tract, there is much more to consider. Healing the gut properly requires a compre­hensive approach that involves five criti­cal components, commonly referred to as the 5R program (Remove, Replace, Restore, Reinforce, and Rebalance). Taken together, this program emphasizes eating the right foods, removing any aggravating substances, as well as supporting the system with the right nutrients. Let’s look at each category in greater detail.

One: Remove

Remove stressors that negatively affect the GI tract environment, including unhealthy, processed foods; allergenic foods; food sensitivities; environmental toxins; and problematic bugs, such as parasites and overgrowth of bacteria and yeast (Candida), which could be causing infections. For more information on testing for GI infections, see the Customer Literature File Laboratory Testing Resources.  

Often people want to skip this step, instead looking for the magic combination of pills that will “just fix it,” but this step is critical. If you are continually exposed to gut stressors, all the gut-healing nutrients in the world will only take you so far because the dam­age will continue to occur. The first things to eliminate are processed foods containing artifi­cial chemicals and ingredients. Choose organic food to avoid pesticides and herbicides, switch to filtered water, and eliminate sugars. Next elimi­nate the foods that you are personally sensitive to. For most people with gut problems, adopting a gluten-free diet is a good place to start, since three out of 10 Americans are sensitive to gluten. After gluten, dairy and grains (including corn) are probably the next biggest culprits; sensitivities to soy are also common. It is common to be sensi­tive to many different foods, especially if your gut problems have been going on for a long time. A Simple Elimination/Challenge Diet can help you identify which foods (including gluten, dairy, grains, and soy) may be triggering symptoms for you. If symptoms continue to persist following an initial Elimination Diet, you might consider exploring and eliminating other, more specific food sensitivities, including high histamine foods, FODMAPS, and nightshades. It might also be pertinent to work with a qualified gastroenterologist or naturopathic doctor who can help identify the presence of parasites, bacterial overgrowth (SIBO), or Candida, which may also contribute to gut symptoms.

Not So Great Grains

There is some good research to suggest that all grains, even whole grains, may not be as health­ful as we’ve been led to believe. Grains contain anti-nutrients, such as phytates. Phytates bind to minerals in the digestive tract, rendering them unavailable for absorption. High intake has been associated with zinc, iron, and calcium deficiencies. They also contain lectins, another anti-nutrient. Lectins compromise the struc­tural integrity of the intestinal lining, increasing gut permeability and encouraging the spread of bad bacteria. Both of these processes ultimate­ly compromise the immune system and are as­sociated with the occurrence of nearly every autoimmune disease. Finally, grains are not really that nutritionally dense. While often being touted as nutritious, all grains are mostly starch and, calorie for calorie, supply far fewer vitamins, minerals, and other phytonu­trients than vegetables and even meat.

Based on these factors, you might con­sider giving up grains completely. Give it time to see how your body reacts. If you choose to in­clude grains in your diet, focus on whole grains like quinoa, brown rice, and buckwheat and properly soak them before cooking to mini­mize the damage. Check out Nourishing Tradi­tions by Sally Fallon for more information on soaking and properly preparing grains.

Two: Replace

Replace digestive secretions that support proper digestion. This includes digestive enzymes, hydrochloric acid, and bile acids, which may be compromised by diet, medications, diseases, aging, or other factors. 

Digestive enzymes aid in the chemical part of digestion, while thoroughly chewing and the muscular motions of the digestive system do the manual part. Those with compromised diges­tion are often lacking in their own production of these important enzymes. Supplement with a broad-spectrum enzyme and remember to take it with meals, since they work by coming in con­tact with foods. You many also choose to take an enzyme supplement containing bile, which supports digestion and absorption of fats and fat-soluble vitamins in the small intestine.

Hydrochloric acid (HCl) is the main component of stomach acid. In addition to helping digest food (specifically, protein), HCl is also important for simulating digestion in the lower GI tract. It does so by signaling the pancreas to release digestive enzymes into the small intestine. It also neutralizes and kills pathogens that enter the body with food, which is important for maintaining bacterial balance within the gut. Aging, chronic use of acid-suppressing medications (like proton-pump inhibitors), and severe H. Pylori infections are all factors that contribute to low HCl levels and encourage the need for HCl supplementation. For dosing recommendations, see the Customer Literature File Acid for Digestion.

Three: Restore

Restore the microbiome (or the community of microorganism that reside within the gut). Help these bugs flourish by consuming probiotic-rich foods and supplements that contain “good” bacteria and prebiotics that good bugs like to eat.

Probiotics are the friendly bacteria, like bifidobacterial and lactobacillus species, that occupy the intes­tinal tract. These bacteria help to keep the in­testines free of undesirable bacteria, make food for the intestinal cells, and even help to make some vitamins. Saccharomyces boulardii is a beneficial yeast that has honorary status as a probiotic. S. boulardii has similar benefits to bacteria-based probiotics but also supports the work of other probiotics by creating an environment that beneficial bacteria can thrive in. It helps to preserve the integrity of the intestinal lining and supports healing of intestinal cells as well.1 There are many different strains of probiotics, which can make it seem daunting to choose a probiotic supplement. Just remember that probiotics from reputable companies are designed to help restore populations of friendly bacteria in your gut. A good way to start is to choose a basic multi-strain, high-potency product in addition to an S. boulardii supplement. Alongside supplementation, focus on incorporating probiotic-rich foods like plain, full-fat yogurt and kefir (if dairy is tolerated); unpasteurized fermented veggies like sauerkraut and kimchi; miso; and kombucha.

Prebiotics nourish the growth of beneficial microbes already in the gut; in other words, prebiotics are food for our beneficial “bugs.” Fructooligosaccharides (FOS) and inulin tend to get a lot of attention as prebiotics, but medicinal and culinary herbs can be prebiotic powerhouses that may have an even greater effect on microbial communities than isolated prebiotics.2 The herb turmeric and the plant compound berberine (found in Oregon grape, goldenseal, and barberry) both appear to be highly impactful prebiotics, promoting populations of beneficial bacteria and the many downstream effects that come with them.3 4 Another underappreciated prebiotic source is chia seeds, which not only contain lots of fiber to feed beneficial microbes, but are also especially high in soluble fiber and mucilage, which help protect the gut lining while also keeping things moving.5

Four: Reinforce

Reinforce gut barrier integrity with a nutritious diet and supplements. Help repair the gut lining by supplying key nutrients that can often be in short supply in a comprised gut, such as zinc, antioxidants (e.g. vitamins A, C, and E), vitamin D, fish oil, and the amino acid glutamine.

Multivitamin. If your gut has been damaged for any length of time, your ability to absorb nutrients has also been impaired and you may be deficient in one or more essential nutrients. A high-quality multi vitamin/mineral serves as a starting point to provide important nutrients like zinc, essential in promoting healthy cells in the GI tract; vitamin A, needed to support mucosal membrane health in the GI tract; vitamin C, support intestinal cell regeneration; and vitamin E, which protects intestinal barrier function due to its antioxidant activity.6

L-Glutamine is an amino acid found abundantly in the body that supplies fuel for the intes­tinal cells, allowing for healthier cells with better absorptive abilities.7

Zinc is necessary for the healing of the stomach lining as well as the intestinal lining. Zinc carnosine, in particular, supports the mucosal cells of the stomach, helping to protect the stomach lining. A number of human clinical studies have found it to be useful for the prevention and treatment of gastritis and gastric ulcers.8 Zinc carnosine also appears to help prevent irritation caused by the use of NSAIDs and modulates inflammation throughout the digestive tract.9

EPA & DHA (Fish Oil) & Vitamin D - Adequate amounts of EPA/DHA (healthy omega-3 fats found in fish oil) and vitamin D are especially important for digestive health. They work via several different mechanisms, including modulating gut inflammation, promoting gut barrier integrity, and supporting and maintaining a healthy gut immune system and microbial balance.10 11 12 Omega 3s (EPA/DHA) are found in especially high concentrations in wild-caught, cold-water fish including salmon, mackerel, and sardines. Salmon & sardines are also good sources of vitamin D, as are dairy, tuna, and eggs. In regard to supplements, cod liver oil provides a great source of EPA/DHA, vitamin D, and vitamin A.

Other Gut Supportive Nutrients & Supplements

DGL (Deglycyrrihizinated licorice) promotes mucus secretion in the stomach lining, protect­ing the stomach and allowing mucosal cells to heal. The effects of DGL are felt quickly and are a favorite of people suffering from heartburn and indigestion.

N-acetylglucosamine (NAG) is a naturally occurring enzyme that helps repair the mucosal lining in both the stomach and the intestines by aiding in the synthesis of the viscous top layer of the gut mucosa.

Gamma-oryzanol, derived from rice bran oil, helps to normalize gastric secretions and has been shown to have a healing effect on the co­lon. A typical dose is 100 mg three times a day for three to six weeks.

Aloe Vera is vitamin-, mineral-, and polysaccharide-rich. It has been used by many tradition­al cultures for digestive complaints of all sorts and is healing and soothing to an inflamed di­gestive tract. Choose a juice that is pressed from the inner filet to avoid the mild bowel stimulant properties the whole leaf can have, and follow the bottle directions.

Many different herbs can be used either in pill, powder, or tea form. Herbs such as fennel and chamomile can inhibit muscle spasms and help to dispel gas and bloating. Peppermint and ginger are traditional digestive tonics, while slip­pery elm or marshmallow have demulcent proper­ties that soothe and nourish the mucus mem­branes of the digestive tract.

Five: Rebalance

Rebalancing involves taking care of your well-being by paying attention to lifestyle choices that support optimal digestive health.

Stress management practices like yoga, meditation, and deep breathing, alongside adequate sleep, healthy amounts of exercise, and quality relationships, can help take us from a chronic fight or flight (sympathetic) state to a state of rest and digest (parasympathetic). This has the sought-after effect of supporting overall digestive health, and thus the health of your entire body.

In conclusion, the good news is that gut cells are very will­ing to heal when given the proper conditions. Following a gut healing routine for three to six months should be sufficient for most people, but be flexible and don’t be afraid to follow that gut feeling!


  1. MacDonald, M. (2019, May 28). Probiotic benefits of Saccharomyces boulardii. Allergy Research Group.
  2. Peterson, C.T., Rodionov, D.A., Lablokov, S.N., Pung, M.A., Chopra, D., Mills, P.J., Peterson, S.N. (2019). Prebiotic potential of culinary spices used to support digestion and bioabsorption. Evid Based Complement Alternat Med, 2019, 8973704. doi: 10.1155/2019/8973704
  3. Ghiamati Yazdi, F., Soleimanian-Zad, S., van den Worm, E., & Folkerts, G. (2019). Turmeric Extract: Potential Use as a Prebiotic and Anti-Inflammatory Compound?. Plant foods for human nutrition (Dordrecht, Netherlands)74(3), 293–299.
  4. Neyrinck, A.M., Sánchez, C.R., Rodriguez, J., Cani, P.D., Bindels, L.B., Delzenne, N.M. (2021). Prebiotic effect of berberine and curcumin is associated with the improvement of obesity in mice. Nutrients, 13, 1436.
  5. Tamargo, A., Cueva, C., Laguna, L., Moreno-Arribas, M.V., Muñoz, L.A. (2018). Understanding the impact of chia seed mucilage on human gut microbiota by using the dynamic gastrointestinal model simgi®. J Funct Foods, 50, 104-111.
  6. Xu, C., Sun, R., et al. (2014). Effect of Vitamin E supplementation on intestinal barrier function in rats exposed to high altitude hypoxia environment. Korean J Physiol Parmacol; 18(4). Retrieved from
  7. Benjamin, J., Makharia, G., Ahuja, V., et al. (2011). Glutamine and whey protein improve intestinal permeability and morphology in patients with Crohn's Disease: a randomized controlled trial. Dig Dis Sci, 57:1000-1012. DOI:10.1007/s10620-011-1947-9
  8. Hudson, T. Nutrient Profile: Zinc-Carnosine. Natural Medicine Journal. November 2013;5(11). Available at:
  9. Whittekin M. Natural Alternatives to Nexium, Maalox, Tagamet, Prilosec & Other Acid Blockers. Garden City Park, NY: Square One Publishers; 2009.
  10. Tabatabaeizadeh, S., et al. (2018). Vitamin D, the gut microbiome and inflammatory bowel disease. Journal of Research in Medical Sciences. DOI: 10.4103/jrms.JRMS_606_17
  11. Parolini, C. (2019). Effects of Fish n-3 PUFAs on intestinal microbiota and immune system. Mar. Drugs, 17(6), 374. Retrieved from
  12. Raftery, T., Martineau, A., et al. (2015). Effects of vitamin D supplementation on intestinal permeability, cathelicidin and disease markers in Crohn's disease: results from a randomized double-blind placebo controlled study. United European Gastroenterology Journal; 3(3):294-302. Retrieved from