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5R Protocol for Gut Restoration

The 5R Protocol for gut restoration was created by the Institute of Functional Medicine as a systematic way to reduce symptoms and restore gut health.

Impaired gut health can present in so many ways including diarrhea, constipation, nausea, vomiting, and reflux. It may also contribute to challenges with mental health by affecting the gut-brain connection and neurotransmitter production.

Wondering what the steps are in the 5R protocol?

Let’s get started!

This information is for educational purposes only. As with any medical advice, always check with your doctor or healthcare professional for personal and age-appropriate recommendations.

What is the 5R Protocol?

The 5R Protocol is a step-by-step process to promote individualized gut healing.

What are the steps in the 5R Protocol to restore gut health? 

Remove for Gut Restoration

What may be contributing to gut irritation? The first step is to REMOVE these irritants.

  • Food
  • Infections
  • Bacteria imbalance
  • Yeast
  • H. Pylori
  • Medications
  • Stress

With food, remove any food that may be causing problems such as gluten, dairy, and processed foods. This is when an elimination diet such as the MRT and LEAP protocol or the Autoimmune Protocol (AIP) may be helpful (1). 

We also want to address any irritants to the GI tract including parasites, bad bacteria, yeast, or H. pylori (2, 3). A functional stool test may be a helpful tool to uncover root causes of GI distress.

Some medications like non-steroidal anti-inflammatories (NSAIDS) may aggravate the gut (4).

Stress also may play a role here so reducing stress by practicing mindfulness, deep breathing, or vagal nerve exercises may be beneficial (5).

This step is when MRT food sensitivity testing and functional stool testing may uncover root causes of symptoms.

Replace: Vitamins That Help with Digestion

Secondly, for optimal digestion, we need to REPLACE anything lacking in the gut which may include digestive enzymes, hydrochloric acid, and bile acids which help to digest carbohydrates, protein, and fat. 

Nutrient deficiencies may also be present with poor gut health.  A micronutrient test is a beneficial tool to analyze vitamins and minerals that are necessary for metabolism, growth, and overall health. Optimize necessary nutrients with supplements like vitamin D, K, B12, magnesium, and zinc if needed (6).

Functional stool testing and micronutrient testing can help to identify deficiencies.

Reinoculate the Gut 

Thirdly, the goal is to expand the diet to create diversity in the diet as balanced beneficial bacteria is necessary to optimize health (7). REINOCULATE the gut with beneficial bacteria and rebuild the gut flora.

Eating more than 40 different whole foods a week (including probiotic and prebiotic foods) can increase the microbiome diversity.

Probiotics are live microorganisms that improve healthy gut bacteria. They support the bacteria that live in us and assist in times of stress to the body such as poor diet, travel, or antibiotic use.

Some probiotic foods and drinks include kefir, kimchi, kombucha, miso, sauerkraut, tempeh, and yogurt. Probiotics may also be in supplement form as bifidobacterium and lactobacillus.

Prebiotics are fibers that stimulate healthy bacteria by feeding the beneficial bacteria. They are food for the microbes that reside in or on us. Prebiotics can be found in bananas, chicory root, garlic, Jerusalem artichokes, and onion.

Essentially, adding probiotic foods as well as supplements can help maintain good bacteria and prebiotic foods feed the probiotics and act like a fertilizer for the good bacteria (8).

Psychobiotics include prebiotics and probiotics that have an effect on mental health through gut-brain signaling (9).

Probiotics and Prebiotics
Probiotics and Prebiotics

A functional stool test can assess gut health and optimize a plan for gut restoration.

Functional stool testing analyzes gut health.

Repair: Best Supplements for Gut Restoration

The next step is to REPAIR the gut for long term gut health. A healthy gut lining is necessary to prevent bad bacteria and toxins from entering your bloodstream and causing inflammation.

One way to repair the gut is by adding supplements like zinc carnosine, antioxidants (Vitamin A, C, and E), and omega-3 fatty acids (10, 11). Some other gut healing supplements may include (12, 13):

A healthy gut is essential for optimizing nutrient absorption.

Micronutrient testing evaluates nutrient needs.


Once our gut is healing, we must choose healthy lifestyle changes to maintain optimal health.  

This final step in the 5R protocol is to REBALANCE your life to keep your newly restored gut healthy (14).

What does balancing your life include?

  • Adequate sleep: target 7-9 hours of sleep, reduce blue light after dark, turn down the lights 
  • Exercise: increasing your activity as tolerated
  • Stress reduction: include meditation, mindfulness, and deep breathing 
  • Healthy relationships: trust, respect, honesty, and communication is important

Try deep breathing, meditation, or yoga nidra.

5R Protocol for Gut Restoration
5R Protocol for Gut Restoration

Final Thoughts

The 5R Protocol is a step-by-step process to promote individualized gut healing.

The 5 steps are:

  • Remove
  • Replace
  • Reinoculate
  • Repair
  • Rebalance

After a gut healing protocol, it is essential to maintain a healthy lifestyle to keep your gut microbiome in good shape.

Every client will have a different 5R Protocol so it is important to work with a clinician to individualize the steps as needed.

Test don’t guess.

Contact me to schedule an appointment to review your personalized nutritional  health.

© Amy Archer RDN, CLT, CHWC


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