The Vital Health “6R” Gut Program: Six Steps to Save Your Health Through Your Gut

Have you tried everything to heal your gut? Or, are you just getting by with a chronic condition like an autoimmune disorder, eczema, or arthritis? Maybe you’ve “gone Paleo,” made buckets of bone broth, said “sayonara” to sugar and gluten, and made friends with sauerkraut. You might have a stockpile (or cabinet!) of digestive enzymes, vitamins, herbs and probiotics… Yet, you are not much better off.

It turns out, when it comes to healing the gut or recovering from chronic conditions, order and timing is everything. We use a 6 “R” Program, along with an individualized treatment approach, to help clients revitalize their health and gastrointestinal function. For those already in the know, this is the latest version of the 4R Program, originally developed by Jeffrey Bland, co-founder of the Institute for Functional Medicine. Here, we’ll fill you in on what the 6R Program is, why it works, and how to avoid some common missteps.

What is the 6R Program and who is it for?

The 6R Program is a systematic, comprehensive approach for restoring your gastrointestinal function, along with a surprisingly long list of other health problems. It’s for two types of people who may think they have nothing in common.

The first type is someone with obvious gastrointestinal distress, who experiences one or more of these symptoms:

  • Gas, bloating, stomach pain
  • Intestinal permeability
  • Constipation, diarrhea
  • Food allergies and intolerances, like gluten and dairy
  • Candida overgrowth, SIBO, dysbiosis
  • Gut inflammation like Crohn’s disease or inflammatory bowel disorder

The second type is someone with stealthier problems that don’t seem related to gut heath, such as:

  • Depression, anxiety, mood fluctuations
  • Achy joints, arthritis
  • Eczema, acne, psoriasis, other skin problems
  • Asthma, environmental allergies, bronchial problems
  • Brain fog, migraine headaches
  • Sensitivity to odors and fragrances
  • Adrenal dysfunction, night sweats, hormonal imbalances
  • Compromised immune system, frequent infections
  • Autoimmune disorders like Rheumatoid Arthritis or Hashimoto’s thyroiditis
  • and more.

The overall health of the gut depends on three things: digestion and absorption of nutrients, elimination of waste including toxins and bugs, and the ongoing maintenance of good gut function

The reason a 6 “R” Program works for both types is that overall health in large part depends on three things happening in your gut. First, your intestines need to digest and absorb the nutrients you eat. Otherwise, even the fanciest shopping cart goods won’t reach your cells. Second, the gastrointestinal system needs to adequately eliminate the toxins, wastes, viruses, and dead cells that are generated as a result of eating and living. Third, the gut needs to avoid becoming inflamed or constipated, because fire and garbage are never a good pair. If these upstream functions don’t work well, you may develop symptoms and disease in the areas of the body that you are most genetically and environmentally susceptible to. That varies from person to person, hence the long list above. Your immune and cardiovascular systems, hormonal balance and nervous system, skin, bones, joints, and even the function of your DNA all depend on a healthy gut.

What are the benefits of a 6R Program?

Simply put, the Program restores healthy digestion, helps you detoxify, and allows the body to rebalance immune function, inflammation, and other key drivers of illness. It can:

“Reset” your GI tract by normalizing digestion, absorption, and assimilation. This reduces gas, bloating and stomach pain, and ensures your body can utilize the food you eat and supplements you take.

Populate your microbiome with probiotic microflora. A healthy microbiome can produce folic acid, other vitamins, and health-promoting short chain fatty acids. It can regulate bowel movements, and influence your weight, nervous system and mood, and prevent the overgrowth of candida and other dysbiotic organisms.

Heal Leaky Gut to restore intestinal permeability to healthy levels. This step can reverse or reduce chronic related conditions like autoimmunity, food allergies and intolerances, inflammation, and immune system dysfunction. Healing leaky gut is also an important piece for those with symptoms who eat fast food or processed foods, drink alcohol, do high-intensity exercise (like long-distance running), are frequently stressed, or who have a history of antibiotic, NSAIDS, or birth control pill use. These factors, and a surprising much more, all influence leaky gut. To learn more, check out our blog: Expanding Our View on Leaky Gut.

Detoxify your body from the inside out by reducing the toxins your gut flora produce from inadequately digested carbohydrates and proteins.

Prevent emergence of diseases in the gut, like SIBO or IBS Crohn’s disease and even inflammatory bowel disease, and beyond, like migraine headaches and hives

Here is a deeper dive into the additional benefits you can get from this program.


Dysbiosis, Candida

6R Program Benefits

  • Restores health-supporting intestinal flora and reduces pathogenic species, fungus and parasites.
  • SIBO
  • Re-locates intestinal flora to proper environment.
  • Food intolerances & allergies, intestinal permeability
  • Supports formation of hydrochloric acid, digestive enzymes, and bile salts. Repairs epithelial tissue.
  • Achy joints, osteoarthritis
  • Reduces the immune system response that drives joint inflammation and cartilage degradation. Supports bone remineralization.
  • Brain fog, migraines
  • Reduces toxic burden, improves absorption of important minerals, and reduces inflammation
  • Eczema, psoriasis, dermatitis
  • Reduces toxic burden and inflammation. Allows skin cells to regenerate and repair.
  • Depression, anxiety, mood fluctuations
  • Improves formation and transmission of neurotransmitters due to adequate food absorption. Improves gut-brain axis function. Reduces toxic burden and CNS inflammation.
  • Autoimmune disorders (e.g. Rheumatoid Arthritis, Hashimoto’s thyroiditis)
  • Normalizes lymphoid tissue and antibody response.

Why does the 6R Program work?

The 6R Program leverages what we know about life in your gut. To get the picture, imagine you have a tomato garden with plants that are under-hydrated, growing in nutrient-deficient soil, and exposed to stress like weather fluctuations. The leafy greens begin to wilt, then yellow, and are eventually overcome by fungus and bugs. Weeds take over and crowd out the plants. How would you turn things around? Would you fertilize? That might help the plants, but give the weeds a hand up too. Would you use pesticides or weed killers? That might help at first, but certain plants and important soil bacteria might die-off, and unless the soil’s nutrients and composition changes, the garden would soon revert. After considerable expense, you might be left tired, frustrated, and with no tomatoes.

Just like a garden, your gut is a habitat. Stress, diet and even how well you hydrate, disrupts things considerably. The 6R Program carefully tends the GI habitat so unhealthy bugs and fungus don’t take over, good (probiotic) bacteria doesn’t die off with the bad, and the gut’s equivalent of soil (epithelial tissue and intestinal mucosa) becomes replete with the right nutrients and substances. In this growing, living, dynamic environment, your intestinal cell walls constantly regenerate. Those new cells can be healthy or unhealthy, and you have a choice over their fate.

The 6R Program restores long-term health by phasing and adjusting interventions as your gut health changes. It usually takes between 3-6 months to complete, which is miraculous considering you are rebuilding your gut, resetting your digestion, overcoming chronic health conditions that developed over years, and changing your life. Severe gut conditions like Crohn’s may take longer.

That said, healing is personal. We don’t have to tell you that. A 6R Program is a foundation that allows other tailored therapies to work. Sometimes it takes more than a 6R Program to meet all of your health goals. However, it’s nearly impossible to initiate the healing process without it. Also, spoiler alert! The Program cannot change a stressful job or home-life. Stress reduction, lifestyle, relationships, and choices that let your “garden” grow, all play a role in how quickly your body can respond to a 6R Program.

One reminder: no need to disrupt what’s working. If the symptoms and conditions above do not apply (lucky you), then a 6R Program is probably not a fit. You can optimize your health with whole foods and recipes, including enzyme-, probiotic- and prebiotic-rich ferments, and addresses nutritional deficiencies with diet and/or supplements. We’d also suggest avoiding parts of the Program while pregnant or breastfeeding due to its detoxifying effects.

What are the 6 “Rs”?

1. Reduce: This is about helping you feel better now so that you have the energy, ability, and motivation you need to put the rest of the plan into action. You’ll reduce symptoms like diarrhea or constipation, and reactions related to certain foods. You might add foods or herbs that calm inflammation, take probiotics or nutrients that are tailored to your needs, like Bifidobacteria for diarrhea, magnesium citrate for constipation, or Saccharomyces Boulardii for candida overgrowth. Or, you might start Epsom salt baths to introduce sulphur and magnesium to aid detoxification or soothe body aches.

2. Remove: There is two side to the removing stage. One side is diet, which plays an important role. While we are big believers of food as medicine, in this stage the magic comes from the foods you eliminate, as opposed to those you add to your diet. The goal? To reduce the burden of irritants and poorly digested foods in your GI tract, to lower inflammation, dampen food allergies and intolerances, and create the space to heal later on. Gas, bloating and stomach pain usually lessens and disappears quickly once the right foods are eliminated.

This is when an elimination diet, oligoantigentic (low allergy), paleo, autoimmune-paleo, Wahls protocol, elemental, Candida, gluten-free, casein-free, Feingold, GAPs, FODMAPS and other healing diets shine. It is helpful to work with an attentive nutritionist or functional medicine provider to determine which diet works best for your needs. You may need to continue a specialized diet until you reach the “Rebalance” phase to avoid the reemergence of symptoms.

The other side is to eliminate pathogenic populations of bacteria, viruses, fungi/yeast (such as candida), and parasites. It often involves taking antibiotic, antiviral, and antiparasitic agents from herbal sources, like oil of oregano or berberine, or pharmaceutical sources, such as Nystatin or Rifaximin.

Pro Tip: Skipping or prematurely ending the “Remove” stage can prolong the time it takes to heal and may lead to symptoms becoming chronic. On the other hand, using therapeutic supplements along with a healing diet can dramatically rev up your progress.

3. Replace: Now you replace or promote substances that are lacking in how you digest, which may be central to how your health and digestive problems began. Options include enzymes, such as proteases, lipases, cellulases, and saccharides, that break down fats, proteins and carbohydrates. These are normally secreted in sufficient amounts from your intestinal walls and pancreas. Other supplements that may be necessary are hydrochloric acid, which is secreted by the stomach for protein digestion to provide protection from various pathogens. There’s also bile, which is secreted by the liver and stored in the gallbladder for use when digesting and utilizing fats.

Pro Tip: Medical herbs, ginger tea, bitters, bitter greens, beets and beet tops, and other foods help may help out a lot here by promoting the body’s ability to produce digestive substances naturally. Though, sometimes in the early stages of a 6R Program even some of these foods may be problematic. An individualized approach is a must.

4. Reinoculate: Enter the mighty microbiome! In this phase, you reintroduce probiotics to reestablish microflora balance. Depending on your progress, it may be helpful to introduce lacto-fermented vegetables like kimchi, sauerkraut, pickles and beets, dairy or non-dairy yogurt, and beverages like kefir and kombucha. It also may be useful to bolster probiotics with foods that contain prebiotics (to feed probiotic bacteria.) These are foods like Jerusalem artichoke, berries, cruciferous vegetables, and fibers like ground flax seeds, beans, lentils, chickpeas, and artichokes. The non-6R Program initiate might make the understandable mistake of introducing these foods and probiotics before removing and replacing, which can result in the return of your original symptoms like gas, bloating, brain fog, or arthritis.

Pro Tip: If you introduce probiotics too soon (by skipping the stages above), you may interfere with an effective “Remove” stage. On the other hand, some may do well with certain probiotic species from the beginning of the program to prevent candida overgrowth. It’s best to get some expert guidance.

5. Repair: Finally, healing begins! Is this stage, you support intestinal cell regrowth, help probiotic bacteria take up residence in your gut, abate inflammation, and establish healthy mucosa with nutrients and foods critical to cell structure, formation, and healing. Favorites are vitamins A, C, E, and D, zinc, glutamine or cabbage juice, collagen or bone broths, amino acids or whey and colostrum (if not allergic to dairy), NAC, glutathione, aloe vera, and mucilaginous herbs like slippery elm and marshmallow root. There are options and it works best to tailor your choices to your particular needs.

Pro Tip: If helpers like slippery elm, aloe vera or marshmallow root makes you feel worse it’s another sign you are moving too fast. Dysbiotic pathogens or yeasts are likely getting fed by the same nutrients you intend for yourself and your probiotic bacteria. In particular, if you experience gas and bloating, it may mean you have SIBO. In cases like this, pop back to Repair.

6. Rebalance: In this stage, you’ll have the capacity to eat more foods than before, along with the energy it takes to throw a dinner party! You’ll be passed any digestive problems you may have had, and may be noticing a lot of other health improvements. You can taper off your “Elimination” phase healing diet, reintroduce foods, expand your diet to meet macro and micronutrient needs, and (re)discover how to eat for pleasure. You’ll also maintain GI health with sufficient fiber, probiotics, hydration, and lots of anti-inflammatory fruit and vegetables. Stress management, mindful eating, and avoiding eating while stressed are also key lifestyle factors for rebalancing and maintaining a healthy gut.

Domenic Pisanelli

Domenic Pisanelli

Domenic Pisanelli is a qualified Naturopath and has helped hundreds of people regain their health back as an experienced naturopath with over 18 years of clinical experience.

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