The 5Rs Of Gut Healing

The health of the digestive system is incredibly important to overall health. The whole body relies on the gut to digest and absorb nutrients for the rest of the body to use in order to grow, repair and to function optimally.

Any imbalance in the digestive system has greater effects on brain health, inflammation, immunity, hormones, detoxification and total body wellness. 

This is why I’m always thinking about the gut when a patient comes to me with a health complaint or disease.

I am considering testing whether they are fully digesting their food and absorbing the nutrition that their body needs. I’m wondering if something is going on in the gut to cause inflammation and symptoms, in the gut or elsewhere in the body since it is all connected. Essentially, I’m looking to uncover their root cause (or causes) and gut health is frequently involved. 

A Functional Medicine 5 R Program is an incredibly helpful framework for healing the gut and supporting a healthy and robust microbiome. 

In this article, you will learn:

  • About common digestive symptoms 
  • Microbiome imbalance, or dysbiosis
  • Reasons behind digestive issues
  • Who benefits from gut healing
  • The details of the 5 R Program I use in my clinic 

Digestive Symptoms 

Digestive symptoms are quite common, although they are likely underreported. Often with mild symptoms, someone may learn to live with it or chalk it up to aging.

For example, it is estimated that GERD, gastro-esophageal reflux disease, affects 18-28% of people in North America and that over-the-counter medications for digestive issues, including acid reflux, are among the top selling categories. 

These statistics are staggering, especially because conventional medicine approaches digestive conditions by suppressing the symptoms- instead of asking the most important question in Functional Medicine: why?. In my view, these symptoms are powerful messages from the body that something is out of balance. And with so many suffering, it must have something to do with the way we are living.

In the initial appointment with a patient, I  inquire about gas, bloating, heartburn, constipation, diarrhea, frequency of bowel movements and other questions to  assess digestion. Whereas many think these symptoms are normal, mild or just part of life, they don’t have to be. 

Interestingly, up to 50% people with COVID-19 experience digestive symptoms. This is a prime example of why investigating digestive symptoms is important instead of simply suppressing them. 


In addition, to experiencing symptom-free digestion, a robust microbiome is foundational for overall health and wellness.

The gut microbiome is the collection of bacteria, yeast, and other organisms that live inside the digestive tract. In a healthy microbiome, the probiotic, or beneficial bacteria, help to keep the opportunistic or pathogenic organisms in check. In an unbalanced system you might find low levels of beneficial bacteria and growth of pathogens. 

Imbalances in the microbiome, or dysbiosis, are associated diseases including metabolic syndrome, asthma, allergies, obesity, immune issues, heart disease and autism. The microbiome is important for growth and development and affects epigenetic expression in the body. New research on the microbiome is continually supporting the idea that the microbiome has a huge influence on health. 


Causes Of Digestive Dysfunction And Dysbiosis

You might be wondering why so many have digestive symptoms of imbalances in their microbiome. Here is a list of common causes:

  • ToxinsToxin exposure can reduce digestive capacity and alter the microbiome.
  • Food sensitivities – Eating foods that you are sensitive to causes inflammation, damages the GI tract and can contribute to “leaky gut,” also known as intestinal permeability, where larger food proteins enter the bloodstream causing an immune response. 
  • Stress – Stress pulls blood from the digestive system and reduces digestive capacity. 
  • Chlorine – Chlorine and other chemicals added to water kill bacteria not only in the water, but in your gut.  
  • Low stomach acid – Low acid impacts the body’s ability to break down food, especially protein, and might be related to age, nutrient deficiencies or acid blocking medications. 
  • Infections – Gut infections, including pathogenic bacteria, yeast overgrowth, H. pylori, parasites and others impact digestive function and the microbiome. 
  • Low fiber diet – Fiber provides food for beneficial bacteria and without enough food, levels decline. Fiber also helps with regularity. 
  • Antibiotics – Antibiotics kill bacteria and often the good guys with the bad. It may take a significant amount of time to recover the microbiome from a course of antibiotics, which is one reason that antibiotics should only be used when absolutely necessary. 
  • Medications – Besides antibiotics, many other medications impact the microbiome or have digestive side effects. These include  NSAIDs (like ibuprofen), birth control pills, reflux medications and more.


Who Benefits From Gut Healing?

With all of these contributing factors to digestive symptoms, dysfunction and dysbiosis, it’s no surprise that gut issues affect many people and are quite often the root cause of health issues. 

Those who have digestive symptoms benefit from a gut healing protocol, such as the 5R approach I am about to discuss.

However, even if digestive symptoms aren’t a major complaint, it is still worth looking at gut health when developing a treatment plan for many other conditions.

For example, autoimmune disease always has a component of leaky gut. 

Here is a list of some of the conditions that may benefit from a gut healing approach:

  • Digestive symptoms: gas, bloating, constipation
  • Leaky gut
  • SIBO – small intestine bacterial overgrowth
  • Candida
  • IBS or IBD
  • Depression and anxiety
  • Arthritis
  • Skin conditions: eczema, hives, psoriasis 
  • Headaches and migraines
  • Memory and cognitive impairment
  • Poor detoxification 
  • Estrogen dominance
  • Poor immunity 
  • Autoimmune diseases
  • Food and environmental allergies
  • Mold toxicity and other toxin exposures 
  • Nutrient deficiencies

The 5Rs – Gut Restoration Program

In my practice, I use Functional Medicine testing including comprehensive stool testing, to get a good picture of what is going on in the digestive tract as far as microbiome health, presence of any pathogens, inflammation and digestive function.

This testing allows me to personalize the 5R protocol for each patient. 

5R stands for: Remove, Replace, Reinoculate, Repair and Rebalance.

Let’s dive into each R now.

1. Remove

Remove refers to removing anything that is irritating or damaging to the digestive system along with treating any infections. 

  • Remove inflammatory foods and foods you are sensitive to. This may require a food sensitivity test or completing an elimination diet. Following a Paleo diet is a good place to start and then the approach can be personalized from there. 
  • Remove food additives and artificial sweeteners.
  • Remove medications, such as NSAIDs, that are contributing to issues. Be sure to talk with your doctor about prescription medication before making changes. 
  • Treat gut infections per testing.

2. Replace

With the remove phase we take out what is not needed and with the replace phase we add in what is missing for healthy digestive function.

This includes:

3. Repair

Repair and heal the lining of the digestive system and correct leaky gut.

Specific nutrients and herbs help support the repair stage:

  • Vitamins including vitamins A, C and D 
  • Zinc (as zinc carnosine)
  • Omega-3 fats
  • The amino acid, l-glutamine, as a supplement and from collagen protein or bone broth
  • Soothing, mucilaginous herbs such as aloe, marshmallow and DGL GI Restore Powder

Combination products, such as GI Restore Powder  include several of these nutrients and herbs in a single formula. 

4. Reinoculate

Reinoculate means to repopulate the beneficial bacteria that make up the microbiome. Testing gives clues about specific levels and imbalances and is useful for recommending specific probiotic supplements and dietary strategies. 

  • Reinoculate beneficial bacteria with probiotic supplements and fermented foods. Small amounts of fermented foods such as sauerkraut, miso and kefir are added to daily meals as tolerated. 
  • Increase prebiotics in order to feed the probiotics, help them proliferate and establish robust colonies. Prebiotic foods include: berries, artichokes, onions, garlic, asparagus, chicory, burdock root, bananas, green banana flour, potato starch, leafy green veggies and others.
  • Including a prebiotic fiber supplement may be helpful for some as well. My Exceed Greens + Reds is a great option; it is an all-in-one option, with pre-biotics, probiotics, digestive enzymes, and fiber.


5. Rebalance

Rebalance means to look deeper into the issues that contributed to the imbalances in the first place and often times these are lifestyle factors. Keep the GI tract healthy and happy by prioritizing sleep, stress management and movement

The digestive system works best when the nervous system is in a parasympathetic or “rest and digest” state. When we are constantly stressed and in “fight or flight” digestion is compromised. Eating while relaxed improves digestion and absorption considerably. Even a few deep breaths before a meal helps.

Also, meditation, yoga, breathing exercises, journaling and other self-care tools have many benefits including maintaining all of the progress you’ve made with your 5 R protocol. 

As a Certified Functional Medicine physician, many people come to me for help uncovering the root cause (or causes) to their symptoms and diagnoses. When I peel back the layers, more often than not, I find gut issues as a contributing factor. This is true for those with digestive complaints as well as those without. 

The goal of the 5R protocol is to heal the gut in order to restore the natural balance to the digestive system. I love this approach, because just like my entire approach to medicine, it is personalized for each individual.

If you suspect you’d benefit from a 5R protocol, you can order testing here or contact my office to set up a consultation.

Healing the gut has benefits throughout the body and remarkably foundational for health and well-being.