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By Lesley Nickleson, RD, IFNCP

Registered Dietitian

“The road to health is paved with good intestines” Registered Dietitians have been saying this for years and now more than ever gut health is becoming a very hot topic in the health and wellness community- and for good reason. Fascinating discoveries about the gut microbiome are revolutionizing medicine, revealing how these trillions of microorganisms living in our digestive tract play a crucial role in everything from digestion to weight management.

Why Gut Health Matters

Gut health refers to the optimal functioning and balance of the gastrointestinal tract and the diverse community of microorganisms residing in it, known as the gut microbiome. It is said that we are more bacterial DNA then we are human DNA in a ratio of 150:1. Our gut microbiome matters!

A balanced and healthy gut will efficiently digest and absorb vital nutrients, effectively eliminate waste and maintain a protective barrier against harmful pathogens and toxins. It plays a crucial role in regulating our immune system, producing essential vitamins like Vitamin K and communicating with the brain through the gut-brain axis to influence our mood. An unhealthy and unbalanced gut can lead to various health issues including digestive disorders, weakened immunity, mental health challenges and even stubborn weight imbalance.

Symptoms of Gut Imbalance

Symptoms are messages from the body. Your body is always communicating with you. The digestive system has many ways to express itself to you, including abdominal pain & discomfort, gas & belly bloating, bowel irregularity with too much, too little, too loose or too hard, acid reflux, mouth sores and even skin rashes.

It is said that 70% of people live with some kind of digestive symptom or disorder.

Poor gut health has been associated with conditions such as acne, rosacea, arthritis, asthma, ADD, autoimmune conditions, depression, eczema, fatigue, migraines, obesity, restless leg and scleroderma, just to name a few.

So what can you do? Enter the 5R Protocol – a comprehensive approach to restoring gut health.

What is the 5R Protocol?

The 5R Protocol is a systematic method used by functional medicine practitioners to heal the gut. It consists of five steps: Remove, Replace, Re-inoculate, Repair, and Rebalance.

Each step addresses different phases of gut healing .

And here’s the thing, there is a certain order of operations in this method. For example, it is important to clean up your diet and provide digestive support, before jumping in and taking probiotics so you are creating a healthy environment for those probiotics to do their job.

Let’s take a look at how this protocol works.

Step 1. Remove

Objective: Eliminate harmful substances that negatively affect gut health. (aka Clean up the Diet)

The first step is to remove food that are harmful to the gut. . This includes pro-inflammatory foods include ultra processed foods (think fast food meal), processed foods with chemical additives, processed meats like deli meats, sausage & bacon, highly refined carbohydrates loaded with refined sugar, non-nutritive sugary foods like sugary beverages, highly refined oils, sources of trans fats (hydrogenated fat) and high alcohol consumption. In some cases where food intolerances are an issue, it may involve the short term removal of common allergens like wheat, dairy, egg, nuts or seafood.

Interesting Fact: Highly inflammatory foods, like refined sugars and unhealthy fats, can disrupt the gut microbiome, leading to ‘leaky gut’ with systemic inflammation. This can exacerbate conditions like obesity, diabetes and heart disease.

2. Replace

Objective: Reintroduce essential components for digestion.

After removing the harmful substances, then it is time to replace substances that support digestion and absorption. This may include digestive enzymes, hydrochloric acid (HCL), bitters and bile acids. These elements help break down food more effectively, ensuring that your body absorbs the nutrients it needs and alleviating symptoms associated with feelings of fullness or heartburn.

Natural sources of digestive enzymes include papaya (Papain) or pineapple (Bromelain). Including plant foods, like mega salads before meals, can help to provide natural plant enzymes. Digestive enzymes and bile acids can also be supplemented to help break down proteins, carbohydrates and fats. This can be helpful if you have had a gallbladder removal.

A practitioner trained in gut health can help you to assess which digestive supports you may benefit from.

Interesting Fact: The simple act of chewing your food thoroughly can activate the release of enzymes to prime your digestive system for nutrient absorption. Therefore I recommend ‘double the chew’ to help aid digestion, ideally 30-40 chews at a time.

3. Re-inoculate

Objective: Restore beneficial bacteria in the gut.

Once we have removed harmful substances and replaced essential digestive substances, the third step is to re-inoculate the gut with good bacteria, also known as probiotics. Probiotics can be found in naturally occurring cultured and fermented foods like natural plain yogurts, kefir, sauerkraut, miso, kimchi, natto and tempeh. They can also be taken in supplement form. I strongly recommend a high-grade quality probiotic that meets third party certification requirements.

Alongside probiotics, prebiotics –food for the beneficial bacteria – should also be included in your diet. These include garlic, onion, leeks, asparagus, banana, oats, apples, flaxseeds, Jerusalem artichoke and chicory root.

Interesting Fact: A diverse microbiome is becoming a new measure of health; microbial diversity = health. Synbiotics are a combination of probiotics and prebiotics to promote the growth of beneficial bacteria in the gut by providing both the bacteria and the nutrients they need to thrive.

4. Repair

Objective: Heal the gut lining.

The stage of repair can be a lot of work, but for some people, in as little as two weeks improvements can be achieved. To repair the gut lining the focus is on targeted nutrients including specific amino acids, vitamins, minerals, omega-3 fatty acids, antioxidants and demulcents.

This includes L-glutamine, an amino acid that fuels the cells of the gut lining, Omega-3 fatty acids for their anti-inflammatory properties and other helpful repair nutrients such as zinc, vitamin D, collagen and bone broths. Gut healing nutrients can be provided in a combination of functional foods and supportive supplements with a personalized nutrition therapy approach.

An equally important consideration is repair of the nervous system. Techniques to help calm the nervous system and shift into a healing response, known as a parasympathetic state. Digestion is a parasympathetic activity.

Interesting Fact: About 70% of the immune system is located in the gut. A strong gut lining acts as a barrier, preventing harmful substances from entering the bloodstream and triggering an immune response.

5. Rebalance

Objective: Achieve and maintain a healthy lifestyle to support gut health.

The final step is to rebalance overall lifestyle to sustain a healthy gut. This involves establishing a

‘new normal’. If you are used to living with chronic digestive symptoms, it is important to adjust to feeling great as the new life takes on a new meaning and purpose. You can now do things that were never before possible. Rebalancing includes managing stress, daily movement, adequate sleep and maintaining a healthful diet rich in fiber, fruits, and vegetables.

Interesting Fact: The gut-brain axis is a communication network that links your gut and brain. This means that gut health can directly impact your mood and cognitive functions. For instance, about 90% of the body's serotonin, a key neurotransmitter that regulates mood, is produced in the gut.


Healing your gut is a journey that requires a comprehensive and systematic approach. The 5R Protocol provides a roadmap to not only address existing gut issues but also to build a foundation for long-term gut health. By removing harmful substances, replacing essential digestive substances, re-inoculating with beneficial bacteria, repairing the gut lining, and rebalancing your lifestyle, you can restore and maintain a healthy gut.

If you have significant gut health issues like irritable bowel syndrome or inflammatory bowel diseases, acid reflux or autoimmune conditions it is best to work with a practitioner trained in the 5R protocol to help guide you through a 5R protocol towards a more positive and healthy life.

Remember, your gut health is intricately connected to your overall health. So, take the time to nurture and nourish your gut, and your body will thank you.



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