Often, gastrointestinal (GI) function must be addressed as the first step to restoring whole-body health and wellness. The 5R Protocol for Digestive Health, offered by Metabolic Maintenance, provides a synergistic, science-based approach to restoring balance to the GI system.

The importance of gut health has recently garnered more attention and focus from the medical research and healthcare professional community, as it has been clearly demonstrated that the gut microbiome responds to the food we eat, influencing obesity, autoimmune disorders, cardiovascular disease, and even mental health.

When the GI microbiome is compromised due to stress, infection, dysbiosis, allergies, parasites, or toxins, local GI symptoms such as diarrhea, abdominal bloating and cramping, acid reflux, and constipation can result. Less local symptoms, such as headaches, lack of focus, mood, immune imbalance, and fatigue can also occur. A compromised microbiome also influences nutrient absorption and can lead to vitamin and mineral deficiencies.

When following the 5R Protocol for Digestive Health, it is important to gradually work through each step and observe your body’s response. Condition-specific healing may take longer and steps may vary or overlap, so it is highly suggested to work closely with a licensed practitioner in these cases.

Each step of the 5R Protocol is designed to address specific problems in the GI system and each ‘Essential’ product has been carefully selected to address one or more crucial factors in each step. Your healthcare practitioner may recommend additional nutrient support and possibly labwork throughout these specific steps based on your individual health. Some of those recommendations are listed for guidance.

Step 1: Remove

Remove focuses on eliminating pathogenic bacteria, fungus, parasites, and viruses from the GI system.* Problematic diets and food intolerances can create unbalanced gut terrain.*

Each of the following can influence GI health:

STRESS – Stress decreases the ability of the immune system to ward off pathogens. Stress can reduce digestive secretions and alter the transit time of food through the digestive tract, thereby changing the balance of intestinal microbial populations and allowing for increased influence from problematic bacteria such as Clostridium.

MEDICATION – Antibiotics, proton pump inhibitors, and NSAIDs are just a few of the common medications that can negatively affect the balance of healthy flora in the microbiome and alter the absorption of vital nutrients needed for optimal GI health.

TRAVEL & IMPORTED PRODUCTS – Due to the globalization of food sourcing and processing, pathogens and contamination that were once only a risk during overseas travel are now increasingly becoming a risk at home as well. The above issues can create unhealthful dysbiosis, however, botanical antimicrobial agents can eliminate pathogens, leaving room for healthful species to repopulate. Effective plant antimicrobials include barberry, Oregon grape, garlic, black walnut, and olive leaf extracts. Happy Belly® contains these herbal extracts as well as caprylic acid to address dysbiosis.


For pathogens: Stool sample analysis, hydrogen/methane breath test.

For food sensitivities: Immunoglobulin food sensitivity test.

Essential Nutrient Support

Happy Belly®

Take 2-4 capsules twice daily (starting with 1-2 per day and gradually increasing). For mild symptoms, continue for 2-3 weeks. For chronic issues, severe symptoms, or moderate to severe overgrowth, continue for 4-8 weeks

Additional Nutrient Support

Metabolic Detox® Complete

Provides 20 grams of pea, rice, and hemp protein, as well as vitamins, minerals, and amino acids to support Phase I and Phase II detoxification for patients who need more nutritional support.

Magnesium Citrate

Take 1-2 capsules per day or to bowel tolerance

One of the most popular and easily absorbed magnesium supplements to assist with regulating bowel movements. Magnesium citrate, specifically, acts as a mild laxative by encouraging motility of the gastrointestinal system.

Psyllium Husk

Dissolve 1 scoop in 8 oz water. Take 1-3 servings a day as tolerated

A natural bulking agent that can be used daily for bowel regularity and aid in the binding and elimination of toxins in the GI tract.

Step 2: Replace

Replace refers to the supplementation of digestive factors and/or enzymes when intrinsic secretions may be insufficient or in limited supply. Stress and the resulting sympathetic state runs counter to the digestive process and can result in reduced secretions of stomach acid and digestive enzymes.

Sufficient levels of acid and enzymes are necessary for the complete breakdown of food and to reduce the antigenic properties of dietary proteins and complex polysaccharides. Incomplete digestion of these larger molecules can also lead to unhealthy microbial fermentation. Symptoms of enzyme insufficiency include a prolonged feeling of fullness after a meal, indigestion, bloating, and gas. Enzymes that may need to be replaced include proteases, lipases, and saccharidases, in addition to factors such as hydrochloric acid and pepsin.


Comprehensive stool sample analysis.

Essential Nutrient Support


Take 1-2 capsules per meal

GluDaZyme™ provides a complete spectrum of digestive enzymes including a proprietary dipeptidyl peptidase-IV enzyme blend, amylase I and II, lipase, glucoamylase, cellulase, hemicellulase, lactase, xylanase, and alpha-galactosidase.

GluDaZyme™ is especially helpful for those with gluten and dairy sensitivities.

Additional Nutrient Support

Betaine Hydrochloride with Pepsin

Take 1-5 capsules of Betaine Hydrochloride with Pepsin per meal. Start with one and slowly increase the dose to stomach tolerance. If a burning sensation occurs, reduce dose by 1 or 2 capsules and maintain thereafter

Betaine Hydrochloride with Pepsin supports normal protein digestion. Hypochlorhydria is common after the age of 60 and can result in poor absorption of nutrients. Use during REMOVE, REINOCULATE, AND REPAIR phases, then try to decrease or discontinue use. Continued supplementation may be needed in times of stress, in the elderly, and in those with weak digestion if symptoms of indigestion begin to reoccur.

Step 3: Reinoculate

Introducing desirable probiotics to the intestinal tract replenishes beneficial species, leaving less space for pathogenic bacteria to grow. Healthy microflora increase the availability of vitamins, degrade toxins, and produce short-chain fatty acids (SCFA) that support healthy mucosal cells.

Probiotic supplementation has been shown to be effective in restoring balance to the gut microbiome. While microbial imbalance has been linked to health issues in areas such as mood, skin, energy, and immunity, a stable and diverse microbiome is associated with the most robust overall health.

Supplementation with a diverse array of microbial strains offers a wide variety of benefits. Lactobacillus strains acidophilus, plantarum, and salivarius, as well as Bifidobacterium strains breve and lactis, are just a few of the many effective probiotics that can be used to reinoculate the intestinal tract and promote GI restoration.

During Reinoculate, prebiotic nutrients are another consideration. Prebiotics are food ingredients that selectively stimulate the growth of beneficial bacteria.

Essential Nutrient Support

BioMaintenance™ Shelf Stable Probiotic

Take 1-2 capsules per day with food

This product delivers high potency doses of shelf-stable probiotic strains.

Additional Nutrient Support

BioMaintenance™ Prebiotic + Fiber

Take 1 scoop stirred into water once a day

Aids in establishing a more healthful microbiome. It contains a synergistic blend of soluble fibers that positively influence the microbial makeup of the gut.

Saccharomyces Boulardii

Take 1 capsule per day

Helps to balance microbial populations in the gut. A beneficial yeast that is resistant to antibiotics, stomach acid, and temperature change, can support the health of your bowels when traveling or using antibiotics. Due to its antifungal properties, it has beneficial effects against Candida yeasts.

In addition, this strain benefits the integrity of both the intestine and the immune system via several different biological mechanisms.

Step 4: Repair

Once harmful influences to the digestive tract have been removed and healthy flora has been reestablished, it is time to REPAIR the GI mucosal cells. Increased permeability at the mucosal border (called “leaky gut”) can be the result of chronic stress, nutritional insufficiency, xenobiotic exposure, food sensitivities, dysbiosis, infection, and inflammatory bowel disease. Supplementation of specific nutrients can be critical in regenerating the mucosal barrier for proper structure and function.

L-Glutamine is a vital nutrient for the promotion of mucosal regeneration. It can induce the expression of specific genes involved in the growth and differentiation of cells in the small bowel mucosal brush border.

Products selected for the REPAIR phase can be started at the end of the REMOVE phase and continued for 4-8 weeks.

Essential Nutrient Support


5-15 g or as prescribed by a physician based on therapeutic need

L-Glutamine supports GI mucosal integrity via tight junctions, regulates inflammation, modulates cellular stress, and supports intestinal glutathione synthesis.*

Additional Nutrient Support


Take 1-2 capsules per day

NAC is an antioxidant supporting the integrity and function of intestinal mucosa.

Deluxe Scavengers™

Take 2 capsules per day

Deluxe Scavengers™ is an antioxidant formula providing a wide range of ingredients such as vitamins A, C, and E as well as CoQ10 and glutathione, for support against oxidative stress and free radical damage.

Vitamin D-3

Dosage is dependent on individual vitamin D status

Vitamin D-3 is a critical nutrient for immune system function and wound healing, and contributes to repair of the mucosal lining. The deficiency of this nutrient has been linked to a variety of GI conditions.

Step 5: Rebalance

Health in the GI system cannot be sustained without maintaining balance in the whole person. A nutritious diet, regular exercise, restful sleep, and stress management are all essential components to the restoration and maintenance of health.

Looking specifically at the gut, stress reduction may be a significant factor for improving one’s microflora balance, increasing innate digestive secretions to metabolize foods, and improving intestinal permeability/barrier functions. To complement your stress management practice, supplemental nutrients and botanical extracts can mitigate cortisol elevations and can improve neurotransmitter release along with the enteric and central nervous system for healthy digestion.

When life gets stressful, changes in digestion affect optimal nutrient absorption. MetaCalm® provides the amino acid building blocks and the necessary vitamin and mineral cofactors to help the body’s synthesis of both mood-enhancing and calming neurotransmitters.

Essential Nutrient Support


3 capsules 1-3 times a day depending on therapeutic need

Nutritional blend to support calming inhibitory neurotransmitters.

Additional Nutrient Support

Anxiety Control Plus

Take 2 capsules 1-2 times per day as needed for a balanced mood

Anxiety Control Plus is a non-sedating formula, gentle enough to use during a stressful day to support a relaxed sense of being. In the evening, ingredients like magnesium and glycine help quiet the mind, relax muscles, and improve quality of sleep.

R.E.M. Maintenance™

Take 1 scoop 30 minutes before bed for restful sleep

Non-habit forming sleep support supplement and provides nutrients that promote both physical and mental relaxation.


The Fullscript Integrative Medical Advisory team has developed or collected these protocols from practitioners and supplier partners to help health care practitioners make decisions when building treatment plans. By adding this protocol to your Fullscript template library, you understand and accept that the recommendations in the protocol are for initial guidance and may not be appropriate for every patient.

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