5-R Protocol For Gut Health

The 5-R protocol is one of the best approaches you can take to heal digestive problems for good. From IBS, SIBO, and GERD to celiac disease, Crohn’s, and ulcerative colitis, the 5-R protocol can help regulate your gut health.



Our GI system plays a role in our overall health of both body and mind. The importance of gut health is more understood than ever, and many healthcare professionals are beginning to focus on how the gut microbiome influences physical and mental health.


The 5-R protocol is a synergistic approach focused on restoring the balance to your GI system. Each step of the protocol is designed to specifically address different parts of the GI tract to help restore your whole body’s health and wellness.




The 5-R protocol is a way to help restore your GI system’s natural balance. Even people with a typical lifestyle can have problems with their GI system; it’s a complex environment and is the main means of communication between our body and the outside world. There are pounds of bacteria in your gut and digestive enzymes used to break down food. The 5-R protocol focuses on bringing the various functions of your gut back into balance.


Let’s break down the five R’s that make up the 5-R protocol.




The first R is remove—we want to remove anything that’s irritating the gut, including:


  • Foods that irritate the gut, like caffeine, alcohol, food additives, and processed food. It’s possible that your gut has a difficult time digesting specific types of carbohydrates. Or food intolerances, sensitivities, and allergies can affect your gut’s health. If you have any of those conditions, following the five R’s and a gut-healing diet can help.


  • Medications and supplements, like NSAIDs and antacids. OTC medications like aspirin, ibuprofen, and heartburn remedies can cause digestive dysfunction. It’s also possible that side effects from your prescription medications can affect your gut health. In addition, many supplements sold in stores can cause digestive issues. However, don’t remove any medications from your routine unless your physician agrees that it’s safe to do so.


  • Stress—it’s more than a feeling. While not easy to remove, stress causes a reaction in your body and releases the cortisone hormone into your bloodstream. If you have too much of this hormone in your system, it can cause inflammation in your digestive tract.


  • Infections, pathogens, and bacteria can all affect your gut health, too. It’s important to seek treatment for any issues that appear to keep your gut in great shape.




Depending on your systems and health conditions, you might be lacking certain elements that are crucial to digestion, like bile, stomach acid, and digestive enzymes. It’s also possible that you’re deficient in some nutrients. The second R—replace—phase of your gut-healing plan might include:


Supplements to replace anything that’s missing. These supplements can replace elements like bile salts, betaine HCL, and the enzymes that help you digest carbs, fat, lactose, and protein.

Foods with the nutrients to help produce those missing elements. For example, bitter foods can often help stimulate your digestive enzymes and stomach acid.


Supplements or foods that replenish nutrient deficiencies. Because digestive issues can affect your absorption of nutrients like iron, B12, calcium, zinc, and magnesium, supplements or foods high in those nutrients can help replenish your body and heal your gut.




The elimination diet isn’t meant to go on forever. Once your symptoms show significant improvement, you’ll start introducing foods back into your diet to help rebalance the microbiome. Rebalancing means returning the collection of good gut bacteria that helps your immune, metabolic, and digestive health.


During the third R—repopulate—you’ll start reintroducing two types of food:


Prebiotic foods that gut bacteria love to eat. These foods include carbs like onions, apples, bananas, asparagus, leeks, onions, and more. You’ll likely also start to reintroduce (or increase) the different types of grains, like barley, oats, and seeds that you eat.


Probiotic foods that are rich in beneficial bacteria. While you might already take a probiotic supplement, it’s time to reintroduce fermented foods like water kefir, sauerkraut, kimchi, kombucha, and yogurt.




The fourth R—repair—is the stage when we want to create the ideal environment that supports long-term relief and gut-healing. It’s time to repair the intestinal mucosa and cells, reduce inflammation, and encourage our microbiome to live happily in our digestive tract.


This step includes incorporating into your diet:


  • Foods that are high in zinc and vitamins A, C, D, and E
  • Foods that are rich in amino acids, like bone broth
  • Supplements like L-glutamine, aloe vera, collagen, slippery elm, and marshmallow




Finally, it’s time to rebalance. Our lifestyle habits have a significant influence on our overall health and digestive system. During this phase, you’ll address:


  • Stress management
  • Improving mental health
  • Exercise routines
  • Improving sleep




The 5-R protocol is a GI restoration program. Not everyone will go through all five steps because all of our GI tracts and symptoms are different. For example, someone may have perfect digestion, enzymes, bile production, etc., so they likely would skip over the replacement phase of the protocol.


Sometimes, you’ll go through multiple steps at the same time. For example, during the first R (removal), part of the strategy is removing the undesirable gut bacteria. But whenever we remove that bad bacteria, we want to replace (the second R) it with something else. These two steps typically go together hand-in-hand. What’s crucial is continuing the third stage (repopulation) for at least a couple of weeks after you stop the removal phase.


And the same goes for step four (repair). Your GI tract’s health is dependent on nutrients, and you need to feed it well to ensure you’re getting all of the nutrients you and your gut needs.

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