The Institute of Functional Medicine developed the 5-R protocol, and it’s 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.
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The 5-R Protocol & Digestive 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’s of the 5-R Protocol
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.
1. Remove
The first R is remove—we want to remove anything that’s irritating the gut, including:
2. Replace
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:

3. Repopulate
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:
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4. Repair
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:
5. Rebalance
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:

How Does the 5-R Protocol Work for Digestive Health?
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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