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Crucial steps to healing your gut: the 4R protocol

The intestinal tract is one of the body’s primary physical barriers from the outside world, protecting us from potentially harmful environmental factors passing through the digestive tract, including toxins, pathogenic microorganisms, and other antigens. The intestinal lining consists of a single layer of epithelial cells separated by protein complexes known as tight junctions. In a healthy gut, tight junctions regulate intestinal permeability, selectively allowing the transport of nutrients across the intestinal barrier, while preventing the absorption of harmful substances.

Certain factors such as a poor diet, stress, or infection can weaken the gut lining, thereby increasing intestinal permeability. Increased intestinal permeability can allow foreign substances to cross the gut mucosa and enter systemic circulation, triggering an immune response along with low-grade inflammation.  Any gut reset program should follow the 4 steps listed below in order to restore optimal gut health:

  1. Remove

  2. Replace

  3. Re-inoculate

  4. Repair 


Read on to find out more about these 4 R's for gut reset and why it's imperative that they be completed in order.

1. Remove

The first step should always be to remove any pathogens, along with any inflammatory triggers associated with increased intestinal permeability. Foods to eliminate should include processed foods, poor quality fats and oils, alcohol, inflammatory foods (such as refined sugars, gluten and dairy), along with any foods that you may have a sensitivity to (foods that don't agree with you).  These foods have all been found to be pro-inflammatory and damaging to the gut lining. Swapping out inflammatory foods with nutrient dense and gut-healing foods will help to reduce inflammation and support the healing of the lining of the gut. Bone broths, vegetable broths, and fresh vegetable juices such as celery juice all have healing effect on the small intestine. Foods from the brassica family such as cauliflower, cabbage, kale, garden cress, bok choy, broccoli, and brussel sprouts are also gut healing.

Instead of this

Try this

Refined sugars: Pastries, sugary cereals, candies, sweetened and/or carbonated beverages, foods containing white or brown sugar and high-fructose corn syrup.

Opt for honey, maple syrup or coconut sugar

Trans fats: Margarine, fried foods, baked goods, store-bought dressings and condiments, most packaged foods. Avoid refined oils like vegetable oil, canola oil, sunflower oil, etc.

Opt for grass-fed ghee, avocado oil, extra virgin olive oil, coconut oil, homemade vinaigrettes, and homemade baked goods

Refined carbohydrates: White bread, white pasta made from refined flour, white rice, baked goods, sugary breakfast cereals.

Opt for sourdough or whole grain bread with minimal ingredients, whole grain pasta or lentil/chickpea pasta, whole grain or wild rice, and homemade baked goods with quality ingredients.

Dairy products: Milk and condensed milk, cheese, cream cheese, cottage cheese, yogurt, butter, cream, ice cream.

Opt for pure coconut milk or homemade plant milk.

Another portion of the "remove" step is to clear out the bowel of any parasites, molds, overgrowth of bad bacteria or fungus, heavy metals, toxic chemicals, or infections. These further cause damage to the gut lining, contributing to digestive symptoms and discomforts, leaky gut, and systemic inflammation. Total abstinence from everything that is irritating the lining of the small intestines is important as this enables the tissue to repair itself.  There is no point in trying to heal the gut lining while damage is still occurring through exposure to irritants.


The removal of molds, parasites, or infections from the body should be completed with the guidance of a health professional. The improper treatment of pathogens can lead to the production of dysbiotic biofilms. Biofilms are aggregates of bacteria, fungi, and other microorganisms that live in communities. When biofilms become dysbiotic they are difficult to eradicate and if done so incorrectly, pathogens can burrow deeper into the gut lining instead of being killed off and eliminated.  Pathogen removal should always be completed with the use of a binder to latch onto toxins and remove them from the body.


2. Replace

Our digestive system uses a variety of enzymes along with hydrochloric acid (HCl) to break down the foods that we eat. Many people have enzyme deficiencies, making them unable to adequately digest specific foods or food groups. Research shows that the natural levels of stomach acid (hydrochloric acid) and digestive enzymes decreases as we age, as well as if we damage our gastrointestinal tracts through food excesses, chemical use, infections and stress.

When the stomach isn't acidic enough, the entire digestive system slows down. Stomach acidity affects every stage of digestion. It activates pepsin, the stomach enzyme that digests proteins. It stimulates the gallbladder to release bile, which emulsifies fats. It triggers the release of pancreatic enzymes that break down proteins, starches and fats. Stomach acidity also creates an unfavourable environment for harmful bacteria and parasites. Without adequate supplies of hydrochloric acid, pepsin, and pancreatic enzymes the body cannot adequately break down protein into its constituent amino acids which are the building blocks of every cell in our bodies. 

If your body cannot properly break down foods, then it is not digesting and absorbing nutrients. This contributes to micro-nutrient deficiencies inability of your cells obtaining the nourishment they need to function properly. Many health issues begin because people aren't fully digesting and absorbing their food properly.


Supplements should be introduced in order to support stomach acid production as well as replace lacking enzymes to support digestion and assimilation of nutrients. There are three major types of supplemental enzyme products: pancreatic enzymes, enzymes grown on a fungal base, and plant-based enzymes.

Pancreatic enzymes are usually derived from animal pancreatic tissue. They work well to assist with digestion as well as to help stabilize blood glucose levels. More recently, enzymes have been grown on a fungal base of mycotoxin-free Aspergillus (mycotoxins are substances produced from fungi that are toxic). These enzymes are blended to ensure that they work in high-acid environments like the stomach. Plant-based enzymes, such as bromelain and papain, are protein-splitting enzymes. Bromelain is derived from the green stems of pineapple plants whereas papain comes from green papayas. Protein splitting enzymes help the immune system to become hardier to food sensitivities. Betaine hydrochloric acid is a man-made form of betaine which can be supplemented to increase stomach acid.

There is also a variety of herbs called digestive bitters which can stimulate stomach acid production as well. These types of digestive aids should be taken with food, always at the beginning of the meal for maximum impact. It's important that you consult with a health care professional before starting a new supplement. Keep your eyes peeled for an upcoming blog article that will take a deeper dive into digestive enzymes and digestive bitters.

  Source: Wix

3. Re-inoculate

The third step is to re-inoculate the microbiota with beneficial bacteria called probiotics. Probiotic supplementation has been shown to improve the composition of microbiota by restoring beneficial gut bacteria species. Probiotic supplementation can improve the health of your digestive system by enhancing the secretion of anti-inflammatory substances, supporting immune system function, altering microbial composition, and reducing intestinal permeability. Intestinal microbes play an important role in our ability to fight infectious diseases, providing a front line in our immune defense. Certain species can even increase our absorption of minerals, including calcium, copper, iron, magnesium and manganese.

Probiotics also improve peristalsis and help normalize bowel transit time. Peristalsis consists of the series of wave-like muscle contractions in your bowels which move stool through the digestive tract for elimination. In order for probiotics to have an impact in the body they must arrive alive to their action site, which is why the quality of the supplement is important. Keep your eyes peeled for an upcoming blog article that will take a closer look at probiotics and how to choose a quality probiotic.

Prebiotics work synergistically with probiotics and can be taken together for best results. If you don't have a rich environment for your gut microbes, taking probiotics won't be all that helpful. Prebiotics act like a rich fertilizer, selecting to enrich only the good bacteria in the gut. Many people experience gas and bloating when they start or increase prebiotic-rich food or begin taking prebiotic supplements but these symptoms usually dissipate after a week or so. This is due to the fact that prebiotics are fermented by probiotics. This fermentation—which occurs quite quickly despite sounding like something that takes months, not minutes or hours—creates gas. To reduce these side effects, start slow and small and gradually increase your prebiotic intake.

While you cannot get enough probiotics to re-inoculate the gut simply through diet, incorporating probiotic-rich foods is a great way to further support your gut. These foods include, fermented vegetables and soy products like tempeh, miso, sauerkraut and kimchi; as well as kombucha, a fermented tea.

4. Repair

The final step involves repairing the gut lining with specific nutrients and medicinal herbs that have been shown to decrease intestinal permeability and inflammation. The surface microvilli in the small intestine are highly regenerative. If given a total rest from everything that irritates them, individual microvilli can repair themselves within 4-5 days. However if the damage is extensive and there are deeper tears in the intestinal wall, healing can take much longer.  It's important to note that depending on the extent of damage to the gut lining, healing the gut can take anywhere from 3-6 months and does require a personal commitment.

Examples of gut healing compounds include: glutamine, zinc, omega-3 fatty acids, colostrum and quercetin. Cells of the small intestine depend on glutamine, especially as their main fuel and for maintenance and repair. Herbs that support gut healing include licorice, marshmallow root, slippery elm and aloe vera. These herbs have a demulcent quality allowing them to sooth irritation of the mucous membranes in the gut by forming a protective film. Keep your eyes peeled for an upcoming blog article that will delve further into these gut repairing herbs and supplements.


Let's recap

A variety of dietary and lifestyle factors such as a poor diet high in processed and inflammatory foods, stress, infection and exposure to harmful chemicals, compounded over time due to ongoing exposure, will damage the gut lining contributing to a leaky gut. A leaky gut allows food particles and pathogens to cross through the gut lining and enter circulation in the bloodstream where the immune system mounts an immune system attack, resulting in widespread inflammation and contributing to a number of associated health conditions. The goal of the 4 R's approach to healing the gut is to minimize factors that lead to increased intestinal permeability and inflammation, as well as introduce factors to help heal your digestive system and improve gut health.

Bear in mind that your gut health affects your overall health. If your gut is out of balance, you can experience unwanted symptoms above and beyond digestive discomfort, which could include hormone imbalances, poor mental health, skin problems, joint pain, and more. Remember, when working to improve your gut health, you are working on bringing your body back into balance.

A note from Kim

If you think you could benefit from the 4R protocol, send me a message! I'd love to chat and determine if introducing dietary supplements to your wellness plan is appropriate for you. I offer single-session private nutritional consulting, as well as have an intensive gut-healing program called Gut Reset Intensive, where we work one-on-one to uncover root cause(s) to your symptoms and to bring your gut back to balance.


Haas, E. M., & Levin, B. (2006). Staying healthy with nutrition: The Complete Guide to diet and Nutritional Medicine. Berkeley: Celestial Arts.

Lipski, E. (2020). Digestive wellness: Strengthen the immune system and prevent disease through healthy digestion. New York: McGraw-Hill.

Papaconstantinou, J. (2022). Symptomatology . Lecture, Toronto: Institute of Holistic Nutrition .

Rowland, D. (2020). Nutritional Solutions for 88 conditions. S.l.: LAP LAMBERT ACADEMIC PUBL.


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