5 R Gut Healing Protocol: Heal Your Gut, Regain Your Health

Poor digestive health symptoms? The 5 R gut healing protocol is for you.

The 5 R gut healing protocol is a framework for addressing a wide range of gastrointestinal problems, with the aim of bringing your gut back into balance.

This is achieved by addressing imbalances in gastrointestinal function, any pathogens and imbalances in the microbiome, and restoring health to the gastrointestinal tract.

5R gut healing protocol blog flyer, probiotic capsules on light blue background

If you are experiencing digestive symptoms like bloating, abdominal pain, GERD, constipation, diarrhoea and flatulence, then the 5 R framework can help eliminate these symptoms.

If your gut isn’t healthy, then not only will your digestion suffer, but your immune system, hormones, brain, nervous and respiratory systems may also not function properly.

Table of Contents

This can lead to various conditions:

and more, showing that gut health is the key to understanding many chronic health conditions.

The 5 R Protocol is a widely accepted clinical guideline developed by the Institute for Functional Medicine (1).

As the name suggests, it involves 5 stages:

1/ Remove

2/ Replace

3/ Reinoculate

4/ Repair

5/ Rebalance

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The 5 R gut healing protocol: Remove

The first ‘R’ is remove.  

This step involves removing any factors that could be interfering with healthy gastrointestinal function, such as:


This means removing all foods that you may be having a reaction to, for example food additives, sugar, alcohol or foods that you may have a food intolerance or sensitivity to, for example gluten, dairy or eggs.

Reactions can cause digestive symptoms like bloating or diarrhoea, or systemic reactions such as increased mucus formation (causing congestion and a runny nose), or immune responses manifesting as skin issues or joint inflammation.

If you’re experiencing chronic symptoms or diseases, then it’s highly likely that there are one or more foods that are contributing to your symptom(s).

Dietary modifications and temporary exclusions of specific foods is often necessary.

This could be the avoidance of, for example:

Or it could involve a more bespoke elimination diet (whilst ensuring nutrient and calorie sufficiency).

Temporary food exclusions are always performed with the aim of reintroducing as many foods as possible back into your diet, at the right time, once the immune response has calmed down and the gut has healed.


Removing potential pathogens helps to:

Unwanted guests in the gut could be bacteria, yeast, parasites or viruses.

Below are some examples of herbs and nutrients that work against each type of pathogen:

Bacteria: berberine, oregano oil, neem, uva ursi, allicin, goldenseal

Yeast: grapefruit seed extract, allicin (from garlic), caprylic acid, saccharomyces boulardii, oregano oil

Parasites: black walnut hull, wormwood, cloves, oregano oil, saccharomyces boulardii

Viruses: olive leaf extract, nano silver, humic acid, monolaurin, lysine


The human gut microbiome can be easily disturbed upon exposure to a range of toxic environmental agents, for example pesticides, plastics (like BPA in plastic bottles), chemicals in cosmetics or unfiltered drinking water.

Removing toxins is a constant work in progress, as they can come in so many different forms, and we’re exposed to thousands of different chemicals daily.

Steps can be taken to minimise our exposure, for example by drinking filtered water, not using plastic water bottles, eating organic, choosing toxin-free cosmetics and personal care products.


Excluding pharmaceutical medications is more difficult, and it’s important you don’t stop taking them without consulting your doctor.

Medications are often critically important for your health. If you are concerned about any medications you are taking, please speak to your prescribing doctor.

But some medications can alter gastrointestinal function.  

Painkillers and anti-inflammatories (NSAID) can be irritating to the gut lining, causing damage to the gut mucosa.

Proton-pump inhibitors (PPIs) are designed to reduce stomach acid production, however the lower stomach acid compromises normal digestive processes.  

Antibiotics, as well as addressing bacterial infections, also kill beneficial bacteria.

Finding the root cause to your problem, and addressing it through a Functional Medicine approach, could mean that some medications are no longer necessary.

The 5R gut healing protocol: Replace

The second ‘R’ is replace.

This step considers what needs to be replaced (or added) to support healthy gastrointestinal function.

What we’re mainly focusing on here is the assessment of, and appropriate therapy for, digestion or absorption insufficiencies.

Signs of poor digestion or absorption include:

Poor digestion can also result in an immune and inflammatory response which can then be associated with many symptoms such as:

Comprehensive stool testing can provide specific details on digestion and absorption efficiency.

In cases of maldigestion or malabsorption, it may be necessary to restore proper digestion by providing supplemental support with digestive enzymes, bile salts or hydrochloric acid (HCl).

Example of specific supplements that may be helpful include:

To support stomach acid levels: Betaine hydrochloric acid, digestive bitters, apple cider vinegar.

To support pancreatic digestive enzyme levels: bitters, pancreatic enzymes (such as protease, lipase, amylase, and other enzymes).

To support bile levels and bile flow: ox bile, choleretics (which increase bile secretion from the liver), cholagogues (which stimulate gallbladder contraction to promote bile flow) for example choline, glycine and taurine.

Optimal digestion can also be supported with mindful eating – chewing your food well, slowing down when eating, and eating in a relaxed environment away from screens, can all support improved digestion.  

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The 5 R gut healing protocol: Reinoculate

The third ‘R’ is reinoculate.

This refers to what is needed to re-establish a healthy balance of microflora and encourage beneficial bacteria to flourish.

The gut is reinoculated with beneficial bacteria, and this is achieved through prebiotic and probiotic rich foods and supplemental support:


Probiotics are live bacteria in certain foods and drinks that provide an astonishing number of health benefits.

You may think of bacteria and other microorganisms as harmful “germs,” but these probiotics are actually helpful.

But these bacteria can improve digestion, reduce digestive symptoms, and help to produce vitamins.

Many of the microorganisms in probiotic products are the same as, or similar to, microorganisms that naturally live in our bodies (2).

The most common bacteria are those that belong to groups called Lactobacillus and Bifidobacterium.

There are many unique strains of Lactobacillus and Bifidobacteria which are commonly available in supplemental form.

Beneficial bacteria can also be found in live yoghurt, cultured vegetables and fermented foods – think of the 4 K’s;  




Krauts (for example Sauerkraut)


Prebiotics are non-digestible food components (fibres) that selectively stimulate the growth or activity of desirable microorganisms.

While there are many types of prebiotics, the most abundant ones are:

Foods rich in prebiotics include:

It is worth noting that some of these are also high FODMAP foods so if you suffer with SIBO / IBS you may have to introduce them slowly.


Synbiotics is the term used for supplements that combine both prebiotics and probiotics.

You may have heard of the term post biotics too – these are essentially the waste “metabolites” left behind after your bacteria digests prebiotic fibres and probiotic foods, and they provide numerous benefits.  

Post biotics include:

The 5 R gut healing protocol: Repair

The fourth ‘R’ is repair.

The repair phase identifies what’s needed to repair and regenerate a healthy mucosal layer and gut lining.

This phase also optimises immune function with specific nutrients and phytonutrients:

Nutrients and foods that support epithelial lining and tight junctions to improve intestinal permeability (‘leaky gut’)

Nutrients that support the mucosal barrier

Demulcent herbs are rich in mucilage (a gelatinous substance produced from plants).

They help to relieve irritation or inflammation of the mucous membranes in the digestive tract by forming a protective film.

These include:

Supporting Secretory IgA (immunoglobulin A)

These are immune cells that provide ‘first line of defence’ immune support in the digestive system, protecting us from pathogens and helping to reduce food sensitivities.

Secretory IgA also helps maintain a balanced gut bacteria community.  

Too high, or too low, levels of secretory IgA can be problematic.

If levels are low, Secretory IgA can be supported with:

If secretory IgA levels are high, it’s important to identify the reason (for instance a gut pathogen, or food reaction) then reduce associated inflammation through anti-inflammatory foods like curcumin (from turmeric) and omega 3 fatty acids.   

The 5 R gut healing protocol: Rebalance

The fifth ‘R’ is rebalance.

The rebalance phase focuses on addressing the whole body health and lifestyle factors needed to support gut healing, and to prevent future gut dysfunction.

The gut microbiome is in constant bidirectional communication with the brain, and factors such as sleep and stress can impact the microbiome and vice versa.


Stress can alter your microbiome composition through stress hormones, inflammation, and autonomic alterations.  

Stress, including episodes of short term acute stress, has been shown to increase our intestinal permeability (‘leaky gut’).

Stress reducing techniques such as breathwork, meditation, being in nature, journaling, yoga can be great at managing the negative consequences of day to day stress.

Herbs can be helpful for supporting the stress response, such as:

Optimal sleep

Optimal sleep is so important because your body moves into the ‘rest, digest and repair’ state (parasympathetic system).

Conversely, poor sleep can worsen symptoms of bloating, inflammation, stomach pains, food sensitivities, and changes to the gut microbiome.

This is why it’s so important to ensure good quality sleep. (5)

Intermittent fasting

Intermittent fasting can improve some specific beneficial bacteria in the microbiome called Akkermansia and Bacteroides fragilis, which exert positive benefits on the gut mucosal layer. (6)


Meditation can positively influence the gut microbiota through the bidirectional cross talk between the gut and the brain (via the vagus nerve) but also directly through the microbiome. (7)


Exercise has many known health benefits.

But when it comes to gut health, exercise has been shown to:

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Timing and sequence of the 5 R protocol

The order, duration and timings of the 5 R protocol depends on many factors.

It’s a flexible framework and each stage can be completed in any order.

When we’re helping our clients to rebalance gut health, we don’t necessarily start with ‘remove’ and go through each phase in sequence.

In our clinical experience, it’s sometimes of benefit for someone to start at another stage, for example the repair stage.

Or there may be more benefit in starting with several of the stages concurrently.

Each case is unique; it depends on the reasons why the 5 R framework is being applied, the symptoms, and the specific gut imbalances.

The 5 R protocol is commonly applied after we have some detailed gut function and microbiome test results, although there can be benefit in performing a more general 5 R protocol in the absence of test results and based on signs and symptoms alone.

Please note however that there are some risks associated with a 5 R protocol and so we recommend you seek professional advice before getting started. 

For example, in our clinics it’s not uncommon for us to hear that people have been taking anti-microbial herbs:

All of this can lead to negative health consequences. 

There’s also an associated risk with taking anti-microbial herbs when you don’t really need to – they of course can help to reduce any pathogenic bacteria / yeast in the gut, but they do also have a knock-on impact on our beneficial bacteria levels.  

If you have symptoms of poor digestive health, the 5 R gut healing protocol is a great framework we use daily in our clinics with great success time after time.

Of course, while the 5 R gut healing protocol provides a useful framework, each case is completely unique, with a unique blend of factors at play.

To your optimised, healthy future,

Lulu & the Coho Health team

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The Institute of Functional Medicine 5 R Protocol [online]. Accessed on 23rd Feb 2023 available at: https://www.ifm.org/news-insights/5r-framework-gut-health/





Aleman, R.S., Moncada, M., Aryana, K. J., (2023). Leaky Gut and the Ingredients That Help Treat It: A Review. Molecules. [online]. Accessed on 28th Feb 2023, available at: https://www.mdpi.com/1420-3049/28/2/619






Mörkl S, Butler MI, Lackner S. Advances in the gut microbiome and mood disorders. Curr Opin Psychiatry. 2023 Jan 1;36(1):1-7. doi: 10.1097/YCO.0000000000000829. PMID: 36131643



Gut microbiome diversity is associated with sleep physiology in humans [online]. Accessed on 23rd Feb 2023 available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779243/



Özkul C, Yalınay M, Karakan T. Islamic fasting leads to an increased abundance of Akkermansia muciniphila and Bacteroides fragilis group: A preliminary study on intermittent fasting. Turk J Gastroenterol. 2019 Dec;30(12):1030-1035. [online].

Accessed on 23rd Feb 2023 available at: doi: 10.5152/tjg.2019.19185. PMID: 31854308; PMCID: PMC6924600.



Ningthoujam DS, Singh N, Mukherjee S. Possible Roles of Cyclic Meditation in Regulation of the Gut-Brain Axis. Front Psychol. 2021 Dec 22;12:768031. [online]. Accessed on 23rd Feb 2023 available at: doi: 10.3389/fpsyg.2021.768031. PMID: 35002859; PMCID: PMC8727337.



Monda V, Villano I, Messina A, Valenzano A, Esposito T, Moscatelli F, Viggiano A, Cibelli G, Chieffi S, Monda M, Messina G. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972. [online]. Accessed on 23rd Feb 2023 available at: doi: 10.1155/2017/3831972. Epub 2017 Mar 5. PMID: 28357027; PMCID: PMC5357536.

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