The 5R gut healing protocol is a five step method designed to heal gastrointestinal (gut) issues from a whole body, root cause approach. These five steps can be used to improve general gut health for a more preventative and proactive approach.

What is the gut microbiome and why is it so important for our overall health?

The gut microbiome is key to every other organ in your body. You can look at it as the key organ that keeps the main system, the entire human body, functioning and healthy. A healthy, well balanced, diverse gut microbiome helps maintain a healthy immune function. It assists in breaking down fiber in addition to producing short chain fatty acids (SCFAs). The gut microbiome produces nutrients like all of our B-Vitamins (when you think of B-Vitamins think of energy!) as well as Vitamin K and helps us absorb minerals such as calcium, magnesium, iron, and zinc. It helps us regulate insulin and glucose levels. It helps us become more resistant to infections or harmful pathogens. Your gut is home to 3-5 pounds of bacterial microbes that live alongside beneficial viruses, fungi, parasites, and worms. These microbes talk to our food. They regulate our genetic expression and inflammation. They help make certain nutrients like B-vitamins for us, they make minerals more absorbable, and they essentially keep the body regulated and balanced.

One of the more important functions the gut has is the production of different hormones and neurotransmitters. We make over thirty different hormones in our gut and they are synthesized by the gut microbiome. These are hormones that regulate our energy, mood, appetite, digestion, and blood sugar levels. Every single neurotransmitter in the human body is produced in the gut and a smaller amount in the brain. That includes our feel-good hormones related to mood and energy like serotonin and dopamine. More than 90% of our serotonin and 50% of our dopamine is produced in the gut microbiome.

The health of your gut, specifically the gut microbiome, is linked to and hugely impacts your mental health because of the gut-brain axis connected through the nervous system via the vagus nerve. Basically whatever affects the gut will impact your mental health, so whenever you are in a funk you can try to rule out poor gut health as a potential root cause. If you are not taking actively care of and prioritizing your gut health you’re missing a huge piece of the puzzle to overall health and longevity. When you take care of your gut health essentially you are taking care of your mood and energy levels which dictate not only the rest of your day but your entire life. Taking care of your digestive health is also crucial to ensure proper absorption of nutrients and to support the immune system.

What chronic health conditions is the 5R Treatment Protocol most effective for?

• Irritable Bowel Syndrome (IBS)
• Small Intestinal Bacterial Overgrowth (SIBO)
• Small Intestinal Fungal Overgrowth (SIFO)
• Gastroesophageal Reflux Disease (GERD)
• Leaky Gut Syndrome or Increased Intestinal Permeability
• Inflammatory Bowel Disease (IBD)
• Celiac Disease
• Inflammation
• Helicobacter Pylori or H. Pylori
• Type 1 Diabetes
• Chronic Fatigue Syndrome (CFS)
• Multiple Sclerosis (MS)
• Rheumatoid Arthritis

One of the best ways to use this guide is to take a preventative and proactive approach to maintaining your gut health before the above conditions appear.

What are the 5 R’s to Restoring your gut microbiome Health?

Remove any pathogens and inflammatory gut triggers.

Alcohol, food sensitivities, food additives (preservatives and emulsifiers in packaged goods), and refined grains/starches and sugar.

Replace whatever was removed with nutrients that support gut healing by reducing inflammation.

Inflammation that often leads to leaky gut syndrome or increased intestinal permeability which essentially is dislodged junctions between the cell walls of the intestinal lining allowing for harmful substances or food particles to pass through the intestinal wall.

Reinoculate or reintroduce the microbiota with probiotic-rich food (think of fermented foods!) or beneficial bacteria.

Prebiotics, Probiotics, Synbiotics, and Postbiotics.

Repair the intestinal lining with specific nutrients, medicinal herbs, and dietary supplements to decrease intestinal permeability and inflammation.

Rebalance all the good habits above into sustainable lifestyle habits.

Consuming a gut healthy nutritious diet, getting consistent high-quality sleep, and finding ways to reduce stress lead to optimal gut health. Rebalance the gut and overall health with sleep to regulate the gut-brain axis, diet to support a healthy gut microbiome, exercise to improve gut motility, and stress management techniques to maintain a balanced and diverse gut microbiome using the tools listed here.

1. Remove any pathogens and inflammatory gut triggers.

Some examples of what to remove are alcohol, food triggers, food additives (preservatives and emulsifiers in packaged goods), and refined grains/starches and sugar. Poor stress management is a non-food related inflammatory gut trigger. Find some ways that work for you to relax your nervous system – some examples include pilates, yoga nidra, breath work, or taking a walk in nature.

• Therapeutic Elimination Diet

• Toxin Binders

• Anti-microbial herbs and supplements

2. Replace whatever was removed with nutrients that support gut healing by reducing inflammation.

A good pantry staple to have is a high quality cold pressed extra virgin olive oil. Not only is it anti-inflammatory but also gut healthy. You can drizzle raw on salads (as well as some raw & unfiltered apple cider vinegar for blood sugar benefits!) or use to cook eggs and sauté veggies.

• Betaine Hydrochloride (HCl) to increase low stomach acid and help overall digestion.

• Apple Cider Vinegar before meals to assist with stomach acid production.

• Digestive Enzymes to optimize digestion.

3. Reinoculate, reintroduce, or repopulate the gut microbiota with beneficial bacteria and support their growth with whole unprocessed prebiotic rich foods along with targeted supplements.

Some examples of gut healthy foods include kimchi, sauerkraut, kefir, homemade kombucha, as well as yogurt. When it comes to purchasing yogurt, I wouldn’t recommend just purchasing any brand off the grocery shelf. Yogurt typically contains live fermented probiotic (beneficial microorganisms) strands. Different strands of bacteria within the yogurt are helpful for different reasons. Number one rule is to avoid the yogurts with any added sugar as that will mess with your gut microbiome. Number two rule is to ideally make your own probiotic rich yogurt. That way you can customize the yogurt based on the beneficial probiotic that you choose to add. *Different probiotic strains are used for different reasons and each have their own unique benefits!*

Link to homemade probiotic-rich yogurt here.

Homemade yogurt is ideal since there is no transit time and you can increase the fermentation time which leads to additional probiotics. You can customize the yogurt based on the probiotic strains that are ideal for your gut condition and you can add some fermented berries on top without worrying about high fructose corn syrup or cane sugar that is often added to conventional yogurts which disrupt the gut microbiome. One of my favorite high-quality yogurt brands is White Mountain Organic Bulgarian Yogurt which you can find at most grocery stores.

I recommend homemade kombucha since store bought can have up to 20 grams of added sugar per bottle which will disrupt the gut microbiome. Homemade kombucha contains zero added sugars because during the fermentation process the sugar is consumed by the SCOBY (symbiotic culture of bacteria and yeast) to produce beneficial probiotics.

• Prebiotics: fibers or food that support the health of the beneficial gut microbiota known as probiotics.

Some food sources of prebiotics: garlic, onions, and asparagus.

Supplement forms of prebiotics: Prebiotic Powder Supplement

• Probiotics: beneficial microorganisms that improve the health of your gut.

Some food sources of probiotics: kimchi, yogurt, sauerkraut, pickles with the brine, and sourdough bread.

• Synbiotics: a combination of prebiotics + probiotics that work together to improve gut health and microbiome diversity.

• Postbiotics: the end result of your body digesting prebiotics + probiotics. Postbiotics include various nutrients that help maintain your gut health.

4. Repair the intestinal lining with specific nutrients, medicinal herbs, and dietary supplements to decrease inflammation and intestinal permeability.

Some dietary supplements to help repair the intestinal lining include L-Glutamine, Deglycyrrhizinated licorice (DGL), and Omega 3 fatty acids. With purchasing an omega 3 fatty acids supplement, It’s important to find a high-quality and third-party tested brand that has a higher EPA (stronger anti-inflammatory effect) to DHA ratio for maximum gut healing benefit.

• BPC-157: a gastric peptide that may help repair the intestinal lining,

• L-Glutamine

• S. Boulardii: Probiotic strain.

• Deglycyrrhizinated licorice (DGL)

• Omega 3 fatty acids (dosage, third-party tested brand, 2:1 – EPA:DHA ratio)

5. Rebalance the gut microbiome by maintaining these gut healthy habits and turning them into a sustainable lifestyle change.

A healthy gut microbiome continues as a result of living a consistent gut healthy lifestyle. You can rebalance as well as maintain the balance within the gut microbiome by keeping gut healthy habits like consuming a gut healthy nutritious diet, getting consistent high quality sleep, and prioritizing stress management. Rebalance the gut and overall health with sleep to regulate the gut-brain axis, diet to support a healthy gut microbiome, exercise to improve gut motility, and stress management techniques to maintain a balanced and diverse gut microbiome using the tools listed here.

Tip: Knowing your reasons or motivations for “why” you maintain certain healthy habits even after healing your condition and turning them into daily lifestyle habits is crucial to maintaining long term health and preventing any GI conditions and symptoms from reoccurring. I created a guide for this very reason that you can read here.

What are some diet and lifestyle habits that negatively affect the gut microbiome?

• Chronic emotional, psychological, or physical stress leading to elevated cortisol levels (or extremely low cortisol as a result of chronically elevated cortisol – both leading to adverse GI and hormonal imbalance symptoms. Ideally, you are aiming for balanced or optimal cortisol levels.)
• Lack of daily physical movement or exercise resulting in gut microbiota imbalance and reduced gut motility (gut dysbiosis)
• Excessive amounts of refined sugars in diet. Some examples of refined sugars include granulated/white sugar, high fructose corn syrup, and brown sugar.
• Excessive amounts of refined grains in diet. Some examples of refined grains include white bread, white rice, white flour, and white pasta.

What are some diet and lifestyle habits that positively affect the gut microbiome?

• Positive healthy relationships: a life that includes positive and healthy relationships with family, friends, and your significant other all lead to a healthier gut microbiome because your body is at ease meaning it is, for the majority of time, in it’s parasympathetic state, able to rest and digest the nutrients needed to sustain energy, life, your mood — a state where you are not constantly triggered or in fight or flight mode leading to improper digestion of nutrients affecting your energy levels and overall mood.
• Using a tongue scraper first thing in the morning. When we are asleep, that is the perfect time for our bodies to clean and rejuvenate itself. By using a tongue scraper, you are removing the leftover bacteria buildup – the white coating on your tongue that your body produces overnight – leading to a healthier oral microbiome which leads to a healthier gut microbiome.
• Using a miswak: oral microbiome health 🤝🏻 gut microbiome health.
• Using a squatty potty: It helps GI symptoms associated with gut health by easing constipation, allowing for a faster transit time, and can prevent hemorrhoids from occurring which can be a result of excess straining.
• Using a bidet

How can I heal my gastrointestinal issues with the help of a functional nutrition dietitian?

Each person is unique and this is recognized in a personalized functional nutrition assessment and intervention plan that engages and empowers the patient in this process to restore optimal function, manage symptoms and promote overall health and well-being.

Functional nutrition addresses the whole person, not just an isolated set of symptoms. We look at it from a root-cause perspective and create a focus on prevention through nutrition, therapeutic diets, targeted supplementation, exercise, interpretation of conventional and/or functional lab testing, botanicals, detoxification protocols, and stress management tools.

Overall from a whole body, root cause approach, to heal gastrointestinal issues we would look at using diet therapy, targeted supplements, herbal antimicrobials, specific probiotic strands, as well as lifestyle modifications (sleep, stress, and exercise) to heal your gut.

The duration of the 5R Treatment Protocol is individualized and varies depending on each client’s condition as well as their personal health goals. Speak to your functional medicine physician or functional nutrition dietitian for guidance on dietary modifications and targeted supplement recommendations. Typically, practitioners re-test patients/clients with the GI-MAP test within 3-6 months after implementation of protocol to monitor progress and make changes to the treatment protocol as needed.

By addressing the underlying causes of gastrointestinal issues — through personalized approaches like evidence-based nutrition, simple lifestyle changes, and targeted supplements — functional nutrition aims to bring the body back into balance and resolve gastrointestinal issues at its root.