The 5R Protocol for Gut Repair - by Jenna Volpe RDN LD CLT of Whole-istic Living

The 5R Protocol: A Holistic Approach to Leaky Gut Repair

While millions of people worldwide are starting to dip their toes into the waters of functional medicine and holistic health, I noticed still very few people have heard of the “5R protocol” for gut repair.  Let’s change that!

Whether you’re navigating leaky gut syndrome, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and/or small intestinal bacterial overgrowth (SIBO)… this little-known, cutting-edge 5-part step-by-step gut-healing protocol is not optional, if you ask me…

And while I feel very fortunate to be among the small percentage of health practitioners who are educated on the “5R’s”, I also believe everyone deserves to know about this protocol, so they can make informed choices. 

(Unfortunately, most people don’t know what they don’t know, and mainstream healthcare doesn’t exactly set us up for success in the department of chronic gut issues since the primary focus is on managing acute illness.)

Alas, in efforts to increase awareness and spread the good word about the 5R protocol, make sure to check out my overview of this little-known, cutting-edge gut repair framework below!

Disclaimer:  This article was written for informational and educational purposes. This article is not meant to replace medical advice or nutrition advice from licensed, qualified healthcare providers. Make sure you’re working with a doctor and registered dietitian if you’re navigating gut issues of any kind.

Affiliate disclosure: This article contains several affiliate links. As an Amazon Associate, I will make a small commission on purchases made through my affiliate links, at no extra cost to you!

What is the 5R protocol?

The 5R protocol, aka the “5R approach” or the “5R’s”, is a holistic, multidimensional, functional medicine approach to gut repair.  

  • This framework and term were founded and coined (respectively) by the Institute of Functional Medicine (IFM), an online non-profit organization which provides education and resources for practitioners and patients in the field of functional medicine.

The 5R approach is based upon the premise that we must address all 5 dimensions of gut healing, in order to totally restore gut health.

This framework is also followed by most functional medicine dietitians, although each of us tends to put our own unique spin on it (since there are many ways to heal).  So you’ll likely encounter some different variations of the 5R’s online and in various functional medicine clinics.  

My overview (below) of the 5R protocol is based on my own training and first-hand experiences as both a holistic-minded clinician and a past patient in the field of gut health and functional nutrition.

The 5 R’s of gut health + functional medicine

The original 5R protocol for healing the gut is as follows:

  1. Remove
  2. Replace
  3. Reinoculate 
  4. Repair
  5. Rebalance 

Now, let’s dive into what each one means and what it entails…

How to Heal Your Gut - The 5R Protocol

Step 1: Remove

First and foremost, it’s important to identify and then remove any offending stuff that is wreaking havoc on your gut.

What it means:  In the initial phase of the 5R protocol, you’ll want to remove any and all reactive foods, ingredients, and/or products that contain reactive ingredients from your diet/lifestyle so your gut will have the space it needs to heal and recover. (This is NOT necessarily a diet, but it can still feel overwhelming!)

Removing reactive foods/ingredients can be tricky if you don’t yet know exactly what’s inflaming you, and what isn’t – especially since there are 3 types of adverse food reactions and multiple different types of IBS diets out there.

Once you’ve ruled out the obvious food triggers via the right type of food logging (which I explain step-by-step in this IBS food diary*), you may or may not also want to look into specialty clinical and functional nutrition tests as needed.

  • People who struggle with disordered eating may actually be better off skipping the “remove” aspect of gut repair if they get triggered by dietary restriction or they are not clinically stable.

Enter step two – replace.

Step 2:  Replace

While restoring gut health, you should still be getting enough macronutrients (carbs, proteins, and fats – the only three types of nutrients which can provide energy in the form of calories) as well as micronutrients (vitamins, minerals, antioxidants and amino acids) so you can build and sustain health and wellbeing.

What it means: Replace in this context means to replace a reactive food, product brand, ingredient, or supplement with a non-reactive alternative.

  • For example: If you’ve determined that you’re lactose intolerant and/or sensitive to cow’s milk, but you usually add milk to coffee/tea, smoothies and cereal, you’ll want to replace cow’s milk with a lactose-free or non-dairy alternative that works well for your body.

Replace” could mean supplementing with vitamins, minerals, herbs, nutraceuticals, or even protein powders as-needed.

  • For example: 
    • In the case of a lactose intolerance or dairy sensitivity, if you cut out dairy, you’ll want to make sure you’re still getting enough calcium in your diet from lactose-free and/or dairy-free calcium-rich foods/supplements, depending on what’s relevant for you. (Remember, one size never fits all!)
    • In the cases of a stomach acid deficiency, you may want to “replace” or supplement this deficiency with bitter herbs for digestion.
    • If someone has had their gallbladder removed, they may be prescribed ox bile and/or digestive enzymes* with meals, to help digest fats (versus just going on a low-fat diet indefinitely, since that isn’t nutritionally sound long-term).

Nutritional needs aside, to “replace” in my variation of the 5R protocol can also mean simply finding ways to still enjoy foods you love by replacing one brand with another, if you can find one that’s “you-friendly”. 

  • For example: 
    • On my healing journey, when I found out I had an oral allergy and sensitivity to almonds, I replaced almond milk with oat milk. 
      • That simple swap was a very low-effort, high-impact modification which ended up making a huge difference in my quality of life, for the better – at no expense whatsoever!

Subtraction (removing) without addition (replacing) foods and nutrients on a gut-repair journey could potentially set you up for nutritional deficiencies, unintentional weight loss, and/or even disordered eating.

And while removing and replacing enough triggering foods with non-reactive alternatives can in some cases be enough to get you feeling anywhere from 30% to 90% better, gut repair is like an iceberg in that the majority of healing takes place below the surface (on the cellular level), invisible to the naked eye.  

That’s where step 3 (reinoculate) comes into play…

Step 3:  Re-inoculate 

Did you know your gut microbiome (aka the ecosystem of trillions of microbes living in your gut) can make-or-break the entire state of your gut health, and your gut itself?  This is why step 3 of the 5R protocol- “re-inoculate” (or what I refer to as “repopulate”) is so darn important.

To clarify… to truly “re-inoculate” entails a LOT more than just eating yogurt or taking a probiotic supplement!

What it means:  “Re-inoculate” in a nutshell means to optimize your microbiome by increasing the amount of probiotic microbes while reducing the presence of pathogenic (harmful) microbes, simultaneously.  

In other words, you want to be consistently providing your gut with plenty of beneficial probiotic foods and supplements (such as a probiotic sauerkraut), while consuming the right prebiotics (stuff that feeds the probiotic microbes)… while also killing off any “bad” pathogenic microbes that could be disrupting your ability to digest food and absorb nutrients properly. 

  • In Module 3 of my Complete Gut Repair Roadmap online program, I walk my Gut Repair Nutrition Warriors through all of this via a step-by-step process which we collectively refer to as “dismantling dysbiosis”.  
    • Dysbiosis (an imbalance of healthy vs. unhealthy gut microbes) is an underlying root-cause of most types of gut issues. (1)

Re-inoculating can mostly be executed via a combination of dietary modification, the integration of probiotic/prebiotic functional foods, and herbal medicine which can alter microbial balance for the better.  

However, in some cases, you may also need medical intervention via a specific antibiotic (such as in many cases of SIBO).

Step 4:  Repair

Many people think they just need a list of foods (what to eat, what to avoid) – and they will live happily ever after. Or maybe a list of pills to take.  But… that’s actually not how gut repair works!

I’ve found in my clinical practice (over and over again) that most people with gut issues completely overlook the 4th step of the 5R protocol: repair.

What it means:  To repair means to nourish and support your gut with specific types of nutrients and other building blocks your intestinal cells require in order to rebuild your gut lining – one cell at a time – so your gut becomes healthier, stronger, and more resilient. 

A few examples of what this could look like:

(This is also something we cover in greater depth in Module 4 of my Complete Gut Repair Roadmap online program!)

Did you know it only takes less than 30 days on average for the majority of the cells making up the gut lining cells to turnover and regenerate, so we have a new gut lining each month?! (2)

If you don’t properly repair your gut, then simply avoiding foods that trigger your unwanted symptoms and/or taking pills that provide temporary relief is what I refer to as treading water in “Symptom Management Sea.”  (In other words, you’re not healing and not moving forward – just managing symptoms enough to stay above water each day.)

On the other hand, when you properly repair your gut lining by nourishing and supporting it with the right building blocks, over time you may even gain back some or many foods that used to make you sick. 

  • I see this happen often in my functional nutrition clinic. This happens because a healthy gut works properly and does what it was designed to do: process your food and absorb the nutrients, taking in just what your body needs, and removing the rest. 😉 

Step 5:  Rebalance

Rebalancing is all about lifestyle modification. The purpose of this 5th step in the 5R protocol is to reduce stress and support a healthy nervous system, since factors like stress, sleep deprivation, and physical inactivity have been found to play major roles in gut issues. (3, 4, 5, 6, 7, 8).

What it means: To rebalance, in the context of the 5 R’s, is to make lifestyle changes that promote better quality sleep and reduce stress. 

A few examples of rebalancing your lifestyle could include any of the following:

  • Meditation or yoga practice
  • Reiki sessions
  • Acupuncture
  • Myofascial release
  • Craniosacral therapy
  • Massages
  • Walking 
  • A fitness routine
  • Scheduling more downtime
  • Setting healthy boundaries
  • Eating mindfully
  • Journaling
  • Bubble baths

And much more! 

(Pro-tip:  It’s better to pick just one or two of those that resonate most with you, versus trying to do a bunch at once.) 

This step or pillar of the 5R protocol (like all the others) will look different for everyone, depending on which areas of lifestyle need the most modification. Work with your treatment team to determine what’s most in-alignment for you, based on where you’re at on your journey.


The 5R holistic framework is multi-dimensional in that it requires you to look at your diet and lifestyle from all angles. I love this approach because it reminds us that in nature, the whole is greater than the sum of its parts.

Each of the 5 steps (remove, replace, reinoculate, repair, and rebalance) as a stand-alone intervention is not usually enough to fully restore gut health among people with chronic gut issues, but when you put it all together, amazing transformation can happen.

Next steps

The 5R’s are actually the foundation on which my online program, the 6-part Complete Gut Repair Roadmap, was designed and built! If you’d like to learn more and consider becoming a Gut Repair Nutrition Warrior, make sure to check out details below!

Complete Gut Repair Roadmap with Jenna Volpe - Learn More

Leave a Comment

Your email address will not be published. Required fields are marked *