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Gut Healing Protocol

Your gut plays an instrumental role in maintaining balance throughout the body and is responsible for much more than digestion and nutrient absorption. Research consistently finds that poor gut health impacts numerous conditions and may be a root cause of many symptoms. 
In this article, we’ll review the foundational gut healing protocol we use for the members in our functional medicine program to eliminate symptoms and solve hormone, autoimmune, and gut problems at the root cause.

Signs of an Unhealthy Gut

Before we discuss our gut healing protocol, let’s review a few signs that may hint towards an unhealthy gut. For starters, the most obvious signs are the symptoms which have a clear connection to your digestive system:
However, there are many symptoms outside of the gut that may also allude to an imbalance:
Fortunately, you have the power to positively impact the most common causes of poor gut health (i.e. diet, lifestyle, and environment).

Personalized Testing

After an in-depth initial visit with one of our functional medicine doctors, we often order a comprehensive blood test for members to evaluate thyroid health, inflammation, nutrient levels, and rule out a few related autoimmune diseases. For example, celiac disease is a serious autoimmune condition in which a person’s immune system mistakenly attacks the lining of their small intestine. This disease can cause bloating, abdominal pain, diarrhea, and other non-gastrointestinal symptoms like fatigue, anemia, skin conditions, and more.
Another test we highly recommend for certain members (especially those with gut symptoms) is a functional stool test to assess your gut bacteria and evaluate for any signs of parasites, yeast overgrowth, fungi, or viruses.  

Our Gut Healing Protocol

We use our version of the 5R approach for our gut healing protocol. While the specifics vary depending on each person’s clinical history, symptoms, and test results, let’s review what this 5R approach may include.


The first step in the 5R protocol aims to reduce bacterial overgrowth and remove pathogens (the bad guys) with targeted supplements, like our Microbiome Balance. This blend of botanical herbs gently rebalances gut bacteria and effectively reduces digestive symptoms like bloating, gas, constipation, and diarrhea. In this step, we may also recommend removing common food sensitivities, like gluten, dairy, and corn, and other foods that disrupt optimal gut function, like alcohol and added sugar. 
microbiome supplement

Microbiome Balance

Gently Rebalance Your Gut


The second step restores optimal digestion by using tools like digestive enzymes, mindful eating techniques, and vitamin or mineral repletion as needed. We may also recommend interventions like vagus nerve activation to support your body’s “rest and digest” capabilities.
digestive enzyme supplement

Digestive Enzymes

Feel your best after eating


The third step of the 5R process is repairing damage to the intestinal lining. Your intestines contain a protective barrier, or lining, to prevent uncontrolled entry of undigested food, bacteria, and toxins. Diet, lifestyle, and bacterial overgrowth may damage this lining and lead to what is commonly known as a “leaky gut.” Unfortunately, a leaky gut can cause an unnatural immune response and even trigger autoimmune disease. We may suggest making bone broth and taking our Gut Rebalance Powder, which provides healing nutrients like glutamine, aloe vera extract, and zinc to repair and fuel the intestinal lining.
Gut Health Rebalance

Gut Health Rebalance

Optimal gut health is only one scoop away


After a month or two of removing overgrowth or pathogens, optimizing digestion, and healing the gut lining, we reintroduce beneficial bacteria to the gut. In this step, we may recommend fermented foods, prebiotic foods, and upping your fiber intake. Your stool test results also allow us to customize probiotic recommendations for what your gut needs the most. However, our most common and effective probiotics include Megasporebiotic and our Root Probiotic
Root Probiotic


Stronger strains for a stronger gut.


The ultimate spore-based probiotic


In the final step of the 5R gut health process, we aim to rebalance your lifestyle to support whole body health. An effective gut healing protocol should always include lifestyle interventions to optimize sleep, stress, and activity levels. These factors are often overlooked, but play a key role in maintaining progress and providing additional support. 

Key Takeaways

Poor gut health is one of the most common root causes of the conditions we treat at Root. In our functional medicine program, we use in-depth assessments by a Root doctor and dietitian, personalized testing, and tailored diet and supplement recommendations to help you treat your condition and reduce and/or eliminate symptoms. 
Learn more about our membership program. Not ready to take the jump? We combined our three most popular gut health supplements into a Gut Health Bundle for optimal savings and results. 
gut health supplements

Gut Health Bundle

Our 3 most popular gut health supplements bundled together for a 10% savings.

Get to the Root at Home 

Curious about where you should start your functional medicine journey? 

Take our Get to the Root Quiz so you can start working towards reversing disease and optimizing your health at the Root cause.
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