GI Tract Function & Health – Where It All Begins

Part III: The Gut Health Protocol

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In this final section, I’d like to discuss the implementation of a protocol to heal the Gi tract using the 5R treatment program. But first, we should finish Jill’s story.

After my initial evaluation with her, while we were waiting for testing results to return, I started her on an elimination diet (available on our website). This is the most common food plan used in functional medicine to initiate treatment of GI tract symptoms. During the four weeks of the elimination phase, she noticed some mild improvements in her systemic symptoms (like joint pain) but no change in her diarrhea, cramping or bowel habits. Four weeks later we received the results of her advanced GI tract analysis using the GI Effects from Genova. This showed inflammation, bacterial overgrowth and poor absorption of proteins and fats, a common pattern seen in our clinic. So, at this stage, we started to personalize her treatment protocol with antimicrobial and anti-inflammatory herbs. This also resulted in mild symptom improvement. We were making progress, though slowly.

At her third visit, she reported weight loss related to the elimination diet, but her bowel symptoms were still her major issue. She hadn’t removed nightshades yet, a common irritant related to compounds known as glycoalkaloids that in susceptible individuals can cause inflammation. I modified her protocol to include a more specific regimen to treat colitis and recommended she also remove nightshades from her diet. By this time, we had already addressed her nutritional deficiencies discovered on her intake, and I had placed her on a fatty acid protocol customized to imbalances discovered through her initial testing. This combination of therapies seemed to work. By her fourth visit, (six months after her first visit) she reported 80% of her GI symptoms were gone. She could now go out with friends and without fear that she would stool her pants and potentially need to leave the group early. During the next several visits we continued to tweak her protocol based on her therapeutic responses, but her major goal had been achieved.

The 5R Program is a basic algorithm used to treat functional bowel issues. What follows is a discussion of this program. At the end, I will attach a comprehensive guide I’ve put together based on a combination of all the different programs taught through the Institute for Functional Medicine. It will include hints on how to personalize this regimen. This should only be done under the direct supervision of a licensed medical practitioner.


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The 5R Program


These steps address the imbalances we discussed in the DIGIN mnemonic that are discovered through the intake and evaluation process.


The first step in this process is to REMOVE all inflammatory foods, food chemicals, stress and abnormal bacteria and fungal elements discovered on advanced testing. For the majority of patients, a simple elimination diet combined with a basic herbal protocol is all that is needed. The elimination diet can be tweaked based on individual symptoms. For those with histamine type reactions, histamine containing foods also are removed. For those with joint aches and pains, nightshades. The specifics for this are contained in the food plan located on our website.


After the inflammatory foods and microbes are removed, missing digestive enzymes and stomach acid are replaced in the REPLACE phase. The most common nutrients missing are digestive enzymes and gastric acid. As we age, our production of stomach acid and digestive enzymes from the pancreas decreases. This results in improper food digestion and nutrient absorption. Symptoms associated with this include gas and bloating following a meal, undigested food particles in the stool, feeling full quickly and reflux. Pancreatic enzymes are a simple first step in replacement. In order to determine if you have a relative gastric acid deficiency, you can perform a test know as the Betaine HCL Challenge test. A summary of this process is included on the Digestive Health Recommendations guide attached here and on our website.


RE-INOCULATION is the next step. The analogy I like to make compares this to gardening. First, you remove all the weeds and rocks. Then you mix in new topsoil and compost and finally, you place the seeds for the season. The same applies in your GI tract. After weeding and replacing, we replant the proper bacteria needed to maintain the health and function of the GI tract. The two main groups of these beneficial bacteria (called Probiotics) are Lactobacillus and Bifidobacterium. Newer research is focusing on sporulating bacteria as well. In reality, we are supposed to eat fermented foods which are rich in these healthy bacterium. This would be the preferred route for obtaining them but for many, a probiotic is the most convenient way to Re-Inoculate their GI tracts.


REPAIR is the next phase. The one cell thick lining of the GI tract is one of the most important interfaces in the entire body. It has the complex job of keeping toxins, undigested food particles and foreign materials as well as harmful bacteria and yeast out of your body while allowing digested food and liquids into your body and access to your immune system. It’s amazing that the system works so well. But for some, this barrier has broken down and now is allowing undigested food or toxins access to your blood and immune system. The Repair Phase attempts to heal this lining. Typical nutrients used in this process include glutamine, zinc and Vitamin A but there is a whole cadre of demulcents and membrane repairing nutrients that can also assist in the healing process.


REBALANCE/RECONNECT is the last phase. This can best be thought of as the maintenance phase. How do you maintain the gains obtained by the four proceeding phases in the 5R Program? For some, this is the most difficult part of the entire process. It includes stress reduction, adequate restorative sleep, maintenance of healthy dietary changes, to list a few.

I have compiled a complete GI guide (below) based on research from the Institute for Functional Medicine. I have attempted to guide individuals through the maze of determining their own GI Protocol. For many, this will be adequate, but some will require advanced testing and a more comprehensive individualized approach including advanced gastrointestinal and nutritional testing. These will require the assistance of a functional medicine practitioner.


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My hope is that this three-part series and the guide below will be beneficial in your own personal health journey and that through continued diligence and attention you can gain and maintain your health for years to come.


Yours in Health,
Aaron Hartman MD