4 Steps to Repairing the Gut (The 4 R’s)



In the functional medicine realm, “The 4 Rs” protocol is an incredibly powerful tool to heal and protect your gut when there is an imbalance.  As a barometer for you to use, your gut is probably in good shape if:

  • You feel good after eating
  • You have 1-3 bowel movements per day (solid, well-formed stools)
  • You do not notice undigested food in your stool
  • You do not need any digestive medications
  • You do not experience GERD or acid-reflux symptoms
  • You do not have gas or bloating following eating
  • You do not have pain or cramps following a meal

On the other hand, you may have poor gut health if you happen to have any of the following signs:

  • Acne
  • Anxiety
  • Arthritis
  • Asthma
  • Autoimmune Diseases (Lupus, Psoriasis, Rheumatoid Arthritis, Eczema, MS, Hashimoto’s, etc.)
  • Belching
  • Bloating
  • Blood Sugar Disorders
  • Cancer
  • Chronic Cough
  • Chronic Fatigue Syndrome
  • Congestion
  • Constipation (less than one bowel movement per day)
  • Depression
  • Diarrhea
  • Dizziness
  • Fatigue
  • Fibromyalgia
  • Frequently Illnesses
  • GERD (heartburn)
  • Headaches
  • Hormone Imbalances
  • Infertility
  • Insomnia
  • Intestinal Spasms
  • Irregular Periods
  • Joint/Muscle Pain
  • Low White Blood Cell Count
  • Mood Swings
  • Nausea/Vomiting
  • Runny Nose/ Stuffy Nose
  • Seasonal Allergies
  • Stomach Pain
  • Thyroid Imbalances
  • Unexplained Weight Loss
  • Weight Gain

The protocol is broken up into 4 steps: Remove, Replace, Reinoculate, and Repair.  Note that while these are broken up into four separate steps, some of them can actually occur simultaneously, depending on the condition


The first phase of this program focuses on eliminating pathogens and addressing the dysfunction of the gut caused by bacteria, fungi, yeast, parasites, and or viruses. This step also includes the elimination of food sensitivities that can trigger inflammation as well as anything coming in with the food such as toxins or molds.  This is can be done by following an elimination diet.  If you have a good feel for your body and are in tune with what you eat, you may already have a good sense of which foods can cause you problems.  Also, avoiding gastric irritants such as alcohol, caffeine, and drugs will be of great help.  Removing these food sensitivities will play a key role.  Then, we can incorporate a variety of different antimicrobials (like black walnut, tea tree oil, Goldenseal, white willow bark, Genetian, oregano oil, and lavender oil) help get rid of the harmful pathogens.



This stage consists of replacing enzymes that are either not present or at less-than-optimal levels in the gut.  These enzymes are needed for vital for proper digestion and absorption of vitamins, minerals, and other nutrients.  You ever hear the phrase, “You are what you eat?”  Actually we are only what we can digest and absorb.  There are many reasons these enzymes might not be at their proper levels.  Possible causes can be poor diet, chronic diseases, aging, and drug use.  Some of the digestive enzymes that might be helpful during this phase include hydrochloric acid (HCL), bile acids (ox bile), proteases, pepsin, and other digestive enzymes.  These are required for proper digestion.  HCL is particularly important in over 60 years old, as our stomach acid reduces with the aging process. Low HCL levels are commonly associated with gastrointestinal dysfunction and disease like SIBO, IBS, and autoimmune conditions.



“Reinoculation” refers to the support and reestablishment of the microbes in the gut.  This imbalance of microbes was what led to dysfunction in the first place!  Probiotics, such a bifidobacteria and lactobacillus species will support this process.  Additionally, Saccharomyces boulardii is a probiotic yeast that can aid in restoring balance in the gut.  Additionally, prebiotics can also be used, as they provide the “food” the probiotics need to survive and thrive.  Changes in your diet will allow strains of good bacteria to get the food they need (prebiotics), while simultaneously “starve out” some of the more harmful strains that may be causing your symptoms.  You can get the prebiotics you need from you diet by eating foods high in fiber, such chia seeds, artichokes, endives, avocados, beans, lentils, and green leafy vegetables.  Important note here: if you start taking probiotics before the symptoms have resolved, you may make matters worse.  Therefore, I highly recommend you work with a healthcare provider throughout this process.



Finally, it is important to provide the nutrients needed to repair, health, and soothe the now-healing gut.  Supporting the gut in this stage is necessary to prevent future gastrointestinal dysfunction and chronic diseases.  There are many nutrients needed in this process, but some are vital in keeping the gut healthy.  For example, L-glutamine is the main fuel of the cells that line the gut wall, and it plays a critical role in repairing the intestinal barrier and “leaky gut.” Other key nutrients include zinc carnosine, omega-3 fatty acids, and Vitamin C.  Some botanicals can be helpful during this stage as well, such as deglycyrrhizinated licorice (DGL), slippery elm, and aloe vera.


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