Nutrient Solutions to Complement the 5R Protocol: A Comprehensive Approach to Maintaining Gut Health

The Institute for Functional Medicine developed the 5R Program, a framework for addressing leaky gut and other gastrointestinal concerns. This program focuses on five areas of health that can be individualized based on a patient’s unique symptoms and health needs: Remove, Replace, Reinoculate, Repair and Rebalance.

The cornerstone of any plan of care incorporates a healthy diet and lifestyle changes. Removing triggering or offensive foods is a hallmark of the 5R protocol, and the practitioner needs to advise the patient about what foods they can and should eat.  The focus should be on whole foods, phytonutrient-rich fruits and vegetables, fiber, and quality fats, choosing organic when possible.  A variety of diets exist that can be tailored to a patient’s individual nutritional needs and health goals.  Three of the most popular include:

  • The Low FODMAP diet
  • The Mediterranean diet
  • The Paleo or Autoimmune Paleo Diet

Evaluating a patient’s nutritional status, symptoms, and dietary history can assist in identifying the most beneficial diet. Considering the diverse food restrictions and allowances inherent in these diets, a patient’s commitment and capacity to comply can influence their overall success.


FODMAP stands for Fermentable, Oligo-Di and Mono-saccharides and Polyhydric Alcohols. FODMAPS encompass foods that can interact with gut microbiota, and through fermentation, can provoke symptoms of discomfort, flatulence and altered bowel habits. Included in this category of foods are lactose, fructose, fructans and other poorly absorbed carbohydrates.

Overall, symptom improvement has been seen in some patients adhering to a Low FODMAP diet, with reductions in abdominal pain frequency and severity, bloating, and improved satisfaction with bowel habits and quality of life, compared to a standard diet consisting of high FODMAP foods.1, 2


The Mediterranean Diet is rooted in whole foods and is abundant in essential fatty acids, with plenty of olive oil, nuts and seeds.  Low in red meat, it emphasizes fresh seafood, dairy, eggs, fruits, vegetables, whole grains, herbs and spices. In an explorative analysis of 68 women from the LIBRE-1 study, researchers observed that the women who adhered to a Mediterranean Diet (n=33) had greater plasma levels of n-3 essential fatty acids and decreased plasma Lipopolysaccharide Binding Protein and decreased fecal zonulin levels, compared to controls.3


This diet emphasizes eating the way our hunter-gatherer ancestors may have eaten. It avoids refined sugars, dairy, processed foods, grains, legumes, soy and peanuts and focuses on all meats, fish, poultry, fruits and vegetables, eggs, nuts, seeds, herbs and spices and healthy fats.  This way of eating can be therapeutic for people who need to remove a wide variety of offensive foods for a period to allow the gut to heal. A meta-analysis of the Paleo diet showed that it can reduce insulin resistance, cholesterol markers, blood pressure and C-reactive protein, making it worth exploring in patients with metabolic concerns.4


Pure Encapsulations provides products for all areas of gut health that can support your patient in every area of the 5R protocol.


In this phase, the removal of processed foods, poor-quality fats, refined sugars, artificial sweeteners, alcohol and possible sources of food sensitivities, like gluten, dairy and carbohydrate intolerances are recommended. The focus should also be on removing stressors, environmental toxins and non-beneficial microorganisms. Supplemental support can include microbial balance, motility support and nutrients that promote liver detoxification.

Pure Encapsulations Nutrient Solutions

  • MotilPro contains ginger extract, 5 hydroxytryptophan, pyridoxal-5 phosphate, and acetyl-l carnitine that provide support for gastrointestinal motility, GI comfort and stimulation of gut-signaling neurons. Suggested use: 2 capsules, 1-2 times daily between meals.
  • MicroDefense w/ Oregano is comprised of a combination of olive leaf, artemisia and clove extracts to promote healthy gastrointestinal tract function and microbial balance and supports immune function and respiratory tract balance. Suggested use: 1 capsule, 1-3 times daily, just before a meal, with 6-8 oz water for 2-3 months.
  • Liver-G.I. Detox contains a nutrient-rich matrix that includes vitamins, minerals, protein, carotenoids and botanical support like chlorella, broccoli and artichoke extracts, along with turmeric and milk thistle to provide dual support for liver and gastrointestinal detoxification. It enhances phase II detoxification enzymes and helps maintain healthy intestinal integrity and proper nutrient utilization.Suggested use: 2 capsules daily with a meal.


The focus should be on replacing processed and poor-quality foods with whole foods and phytonutrients by consuming a wide variety of colorful fruits and vegetables. Hydrochloric acid, bile salts and digestive enzyme support are recommended to support optimal digestion.  Exploring ways to support the patient’s sleep quality, exercise, stress management and work/life balance should also be addressed.

Pure Encapsulations Nutrient Solutions

  • Betaine HCl contains Betaine HCl and pepsin to support healthy gastric function and promote the absorption of protein, vitamin B12 and calcium. Suggested use: 1 capsule, 3 times daily, with each meal.
  • Digestive Enzymes Ultra contains an extensive profile of vegetarian digestive enzymes to support protein, carbohydrate, fat, fiber, and dairy digestion and promote enhanced nutrient bioavailability and absorption.Suggested use: 2 capsules with each meal.


This area explores the use of probiotics and prebiotics to repopulate the gut with beneficial microbes and their metabolites. Cultured and fermented foods may also be used to feed the microbiome, depending on the patient’s tolerance.

Pure Encapsulations Nutrient Solutions

  • Probiotic G.I. provides 10 billion CFU per capsule of the beneficial bacteria Lactobacillus acidophilus, Lactobacillus salivarius, Lactobacillus casei, Bifidobacterium bifidum, Bifidobacterium lactis and Streptococcus thermophilus to promote healthy immune balance within the G.I. tract and help maintain the integrity of the intestinal mucosa. Suggested use: 1 capsule, 1-2 times daily, with or between meals.
  • Poly-Prebiotic Powder is a unique powdered blend of researched prebiotic fibers and polyphenols to support gastrointestinal, cellular and immune function by boosting bifidobacteria and microbiome diversity. Suggested use: 1 scoop, 1-2 times daily, mixed with a beverage or into food.


This area of the program focuses on foods that are easy to digest, provide nourishment and support gut integrity, like bone broths, soups and stews, teas and well-cooked versus raw foods. Medical foods may also be employed during repair.  Supplement recommendations should include nutrients that soothe the GI tract and support the gut mucosa.

Pure Encapsulations Nutrient Solutions

  • Peptic-Care contains a patented 1:1 chelate of zinc and l-carnosine, providing synergistic GI mucosal protection and supports the stomach’s mucosal defenses, buffers gastric acid, maintains healthy cytokine release and provides antioxidant support for the GI tract.Suggested use: 1 capsule, 1-2 times daily with meals.
  • Epi-Integrity Powder promotes healthy modulation of mucosal immune responses to support GI integrity.Suggested use: 1 scoop, 1-2 times daily. Add 1 serving to 8 oz of water or juice.
  • L-Glutamine delivers 850 mg of L-glutamine to support the mucosal lining and healthy functioning of the gastrointestinal tract; it may help to maintain lean muscle mass.Suggested use: 1 capsule, 1-3 times daily, between meals. Also available in powder.
  • SunButyrateTM-TG Liquid provides 875 mg of short-chain fatty-acid butyric acid in one teaspoon to promote gut-barrier integrity, cytokine balance in the GI tract, abdominal comfort and bowel motility.Suggested use: 1 teaspoon, 1-3 times daily, with meals.
  • DGL Plus® contains a synergistic combination of deglycyrrhizinated licorice extract, aloe vera extract, slippery elm and marshmallow root extract to help stimulate the quality and production of stomach mucus, provide nutritional support to the gastrointestinal tract and support the body’s natural defense mechanisms.Suggested use: 1 capsule daily before a meal.


In this stage, the patient should have experienced improvements in their health and the focus is on continued implementation of approaches to reduce stress, maintain sleep quality and support healthy gut function. Reassessing nutrient needs and supplement dosages is recommended, as well as reintroducing some previously eliminated foods to assess tolerance.


Supporting a patient’s gut health requires a multi-layered approach. Following the 5R Framework partnered with Pure Encapsulations premium products can be foundational in a patient’s digestive system balance and improving their overall health.

Pure Encapsulations® provides uniquely formulated products made with high-quality, pure ingredients backed by verifiable science to complement your plan of care.


  1. Varjú P, Farkas N, Hegyi P, et al. PLoS One. 2017;12(8):e0182942. Published 2017 Aug 14. doi:10.1371/journal.pone.0182942
  2. Halmos EP et al.  JGGastroenterology. 2014;146(1):67-75.e5. doi:10.1053/j.gastro.2013.09.046
  3. Seethaler B et al. Eur J Nutr. 2023;62(7):2779-2791. doi:10.1007/s00394-023-03172-2
  4. Sohouli MH, Fatahi S, Lari A, et al. Crit Rev Food Sci Nutr. 2022;62(17):4551-4562. doi:10.1080/10408398.2021.1876625