The 5-R Gut Healing Process


We are not taught about the importance of the gut as we grow up and go through school.  Even doctors and mainstream medicine undermine the role of the gut in health.  But think about this:

  • We obtain energy and the building blocks of energy from food and water
  • 80% of our immune system surrounds our gut and is part of the gut
  • The American culture promotes convenience, but for the gut to work best, we must be relaxed (“rest and digest” is the motto for the nervous system that controls the gut)

In functional medicine we use a process that goes by the simple acronym of the ‘5Rs’: remove, replace, reinoculate, repair and rebalance. With the guidance of the right practitioner, the 5R process can cause significant improvement in symptoms, and sometimes completely reverse the problem.

Functional medicine focuses on FUNCTION, and an improperly functioning gut can lead to a number of symptoms and conditions, including:

  • Fatigue
  • Muscle pain
  • Headaches and migraines
  • Allergies
  • Mood imbalances and memory issues
  • Joint pain
  • Persistent skin issues like eczema and acne
  • Some cancers
  • And, obviously, IBS and inflammatory bowel disease

Addressing the health of the gut is often the first step towards resolving symptoms like those listed above.  

5-R Process Specifics

The list below represents each “R” in the process.  The first two typically must be done before moving onto the last three.
  1. Remove: Remove things that negatively affect the environment of the gut (inflammatory foods, parasites or other “bad bugs”, chronic medication use that causes inflammation – including excessive supplement use, and more).  Removing these things may involve medications or herbs, but always involves removing foods that cause inflammation.  
  2. Replace: Replace “upstream” digestive support, which may include digestive enzymes, hydrochloric acid, and bile support.  A stool test is the best way to determine which form of support may initially be needed, but sometimes a patient’s history can also be a good guide.  For example, many patients with hypothyroidism have low stomach acid production..  Working with a practitioner to replace the acid may be the best first step.  
  3. Reinoculate: Help resident bacteria (aka the “probiotics”) grow and stay around by taking probiotic foods/supplements in combination with prebiotics (probiotic “food”).  Most probiotics only eat fiber found in food (particularly found in vegetables and legumes, which most of us do not eat enough of!). If you want them to say around, you have to feed them! 
  4. Repair: Help the lining of the gut repair itself by supplying healing the gut wall with various herbs, and supplying key nutrients that can often be in short supply when the body is dealing with chronic symptoms.  These nutrients include specific forms of zinc, antioxidants (e.g. vitamins A, C, and E), fish oil, immunoglobulins, and glutamine.
  5. Rebalance: This is entirely dependent on habitual lifestyle choices – good sleep, moderate exercise, continued good nutritional choices, and having a daily stress management habit are all keys towards maintaining good gut health.  In particular, stress management is often forgotten, but the cortisol that is released during persistent stress causes the gut lining to be “thin” and susceptible to damage.
A full 5-R Process takes three to six months to complete. The foundation of the process is dependent on lifestyle habits, and can be a dramatic change from what many are used to.  No pill is going to be the answer – habits (especially nutrition habits) are essential to maintain a properly functioning gut.  
Please note, there is no such thing as a one-size-fits-all 5-R gut protocol.  The repair step, in particular, is where many practitioners (and patients) fall short.  In my toolkit, I have more than 30 options to address this step, but many of the best options are costly and require high doses.  However, there are ways to use food as medicine for this step – dependent on a patient’s food preferences.