The 5 R Gut Healing Protocol

Whether you are dealing with digestion issues, autoimmunity, brain fog, fatigue, or skin issues, the 5R gut protocol could be hugely beneficial to you! The importance of gut health must not be overlooked since it is closely linked to the immune system and is the organ that absorbs most of the vitamins and minerals that we need to thrive. Since our gut highly influences our overall health, it’s essential that we first take care of our gut in the process of trying to heal our symptoms. 

By treating the gut, you can not only help a range of GI symptoms you may be experiencing like reflux, IBS, and SIBO, but you can also improve symptoms like anxiety, depression, acne, migraines, and hormone imbalance.

What is the 5R Gut Healing Protocol?

The 5R gut healing protocol is designed to restore the natural balance of your gastrointestinal tract. Because many of us are exposed to environmental toxins, unclean diets, and daily stress, our gut health is most likely not optimal. We are seeing more unbalanced gut microbiomes in patients, meaning they have more harmful bacteria than beneficial bacteria in their gut. This imbalance can lead to those health issues stated above. 

This 5R protocol focuses on five parts to restore your natural gut balance, including:

  • Remove
  • Replace
  • Repopulate
  • Repair
  • Rebalance


You first want to remove all the stressors that are causing your gut to go into havoc. You can’t truly heal the gut in the long run if your body is still being subjected to the harmful factors that got you into this position in the first place. These may include:

  • Food

Food sensitivities are a major drawback to gut health. The thing with food sensitivities is that many people don’t know they have one. Food sensitivities can cause a variety of symptoms including but not limited to: headaches, acne, constipation and systemic inflammation in your body. 

Over time, interaction with these irritants causes havoc on the gut leading to a wide array of health problems. Some of the most common sensitivities are from gluten, dairy, soy, and eggs, but every person’s body is unique. To know for sure which foods you are sensitive to, you can try the elimination diet or even get a food sensitivity test performed. It’s better to test than to guess if you want the most optimal results. Also, it can help speed up your gut healing protocol if you are avoiding foods that are causing inflammation in the gut.

  • Infections, Pathogens, Bacteria and Parasites

You should be tested for these via stool testing so they can be treated properly.  We will want to eliminate these factors first and foremost since you can’t truly heal your body if your gut has to battle these foreign invaders constantly. There are different protocols to remove yeast, parasites and pathogenic bacteria so work with your provider to get rid of these unwanted imbalances. 

  • Stress

I think most of us can agree that life is stressful! Trying to balance work, home life, social life, kids, etc. is hard. When you are stressed out, your body puts its energy into responding to the stress signals. Your body then unnecessarily overworks your immune system and reduces its attention on your gut. Stress can also weaken your intestinal barrier, allowing gut bacteria to enter into your body.

However, learning how to manage your stress to create a life that is less taxing can be a key factor in enhancing your health. When you take the majority of this stress away, you are letting your body focus on vital factors like gut processes. 

  • Toxins

Toxins in your water, food, and home and beauty products can disrupt your microbiome, killing off the helpful bacteria. When your body is exposed to toxins day after day, they can’t be properly eliminated and they build up in your body. These toxins can disrupt the normal functioning of the gut leading to chronic diseases, allergies, obesity, and other GI issues. 

Be sure to avoid harsh chemicals and replace your products with toxin-free alternatives. Our family’s go to for all things cleaning is Norwex.  



Next, you’ll want to replace missing elements that are vital to digestion. These can include replacing digestive enzymes, betaine HCL, and ox bilex. Ox bile or bile acids, specifically, are critical in digestion since they increase the absorption of fat soluble vitamins. To replace these you can use supplementation specific to your body’s needs. You can also consume foods that stimulate stomach acid and digestive enzymes such as bitters. When you replace these necessary elements, you’ll also be able to break down fats, carbohydrates and proteins more effectively and efficiently. 

Another reason why having an adequate amount of bile is critical is because it plays a role in toxin elimination. Bile is how many dangerous “fat-loving” substances and toxins get excreted from the body. If there isn’t enough bile, toxins may build up, creating even more damage to your gut and overall health. 



The levels of good bacteria in your gut are commonly on the lower end if you are experiencing dysbiosis, otherwise known as the imbalance of gut bacteria. One way to increase good bacteria in your gut naturally is by eating fiber-rich foods and adding in a high quality probiotic to your routine.



Fixing your damaged gut is essential in restoring your overall gut health. This includes repairing your gut lining, mucosa, and inflammation damage. To do so, you’ll want to include more vitamin A, C, E and D, zinc, collagen and amino acids, particularly L-glutamine. Some people do better with immunoglobulins to help heal their gut. I personally love consuming bone broth, which is full of these nutrients and great for gut repair. 



This 5R protocol can’t be successful in the long term if this step is overlooked. You can’t go back to your old way of living, as your gut will go back to that damaged and unhealthy state. To truly rebalance your gut, you need to consider your lifestyle behaviors. For example, the overuse of antibiotics can be detrimental to your health when they are not absolutely necessary. In some cases they are necessary and life saving. 

Healing the gut isn’t a quick fix or fad. It’s a lifestyle choice that gets easier and more enjoyable with time. At first, it may feel like a lot, but with any habit, the more you put it into practice, the more normal and easy it becomes. 

Equally as important as diet in this step, is stress management. You want to help your body get out of that constant, sympathetic, “fight or flight” mode. Ways to do this are by practicing yoga, meditation, breathing exercising, and getting enough sleep. When you do this, you are allowing your gut and gut flora to relax which helps it stay in balance. 

One simple yet effective habit is to practice mindful eating. Simply put this means to slow down, chew your food, enjoy it and be present at meals. This will really help with the digestion and absorption of your nutrients.


This 5R gut protocol isn’t a quick fix or bandaid to “fix” your health issues. It’s a long term solution. You are in control of your own health. You have the decision to focus on your health so that you can live a long, healthy life where you can enjoy life to the fullest. Making healthy choices in your life can change your life for the better.