Heal your gut, heal your life.

That's the new mantra.

The new orthodoxy.

And any orthodoxy deserves skepticism.



The 'heal your gut, heal your life' prescription needs to be thoroughly tested, to see if it holds up.

So, I've been testing it.


  • What does the science say?;
  • What experiences have my favorite healers & optimizers had?; and
  • How does all that fit with what Matthew and I have been learning through our own n=1 experiments, our attempts at biohacking autoimmune and biohacking peak experience~?

Between these three sources, I'm triangulating my exploration of these ideas. Which has resulted in the creation of a Microbiome Protocol.

Though I'm not suggesting we need yet another healing protocol (there's already an abundance of those). Just a meta-protocol. That aligns the various healing and optimization protocols & provides a frame through which to contemplate them.

In that spirit, let's consider the 5 'Rs' of Gut Healing.

But first, a quick diagram of the Microbiome Protocol elements:

The Microbiome Protocol 2

Now let's consider these elements alongside the 5 'Rs':

The 5 'Rs' of Gut Healing

The 5 'Rs' refers to the gut healing principles used in Functional Medicine.

Those principles are: Remove, Replace, Reinoculuate, Repair & Rebalance.


We need to remove everything that negatively affects the gastrointestinal tract.


  • Things we voluntarily consume, like foods that upset the microbiome and cause intestinal permeability;
  • Things we involuntarily introduce, like chemicals that harm friendly microbes; and
  • Any pathogenic microflora lurking in the GI tract, like yeast, parasites or unfriendly (or unbalanced) bacteria.

The removing phase involves a healing diet, like the Autoimmune Protocol, in which all potentially problematic foods are removed.

It also involves removal of chemicals that are harmful to the gut, both external chemicals, like artificial sweeteners, and harmful internal chemicals like excessive cortisol from chronic stress.

It may also involve taking drugs or herbs to eradicate unfriendly bacteria, yeast or parasites. In the event that pathogenic microflora has armored itself inside biofilms, removal also needs to involve eradicating those biofilms, so the microbes inside become vulnerable.

Elements of the Microbiome Protocol covered by the principle of 'removal' include an anti-inflammatory diet, stress management, reduced chemical exposure, mindful drug use & mindful caffeine use.


Replacing restores naturally occurring digestive aids, including enzymes, hydrochloric acid, and bile acids that support proper digestion.

These can be taken in supplement form before eating (& aren't explicitly included in the Microbiome Protocol).


Reinoculation supports and reintroduces beneficial bacteria. Reinoculation includes dietary approaches, like fermented foods, probiotic supplements and resistant starches, as well as medical interventions, like Fecal Microbiota Transplants.

These approaches are covered under 'gut health therapies' in the Microbiome Protocol.

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Take the Assessment

In the case of significant gut dysbiosis, attempts at reinoculation through diet may exacerbate symptoms, for a variety of reasons outlined by Chris Kresser.

Chris notes that "the extent to which you react adversely to probiotics and fermented foods and prebiotics... is roughly proportionate to how screwed up your gut is. In other words, the more strongly you react to these things, the more likely it is that you need them over the long term".


Repair restores of the healthy mucosal lining of the intestinal tract.

This includes supplying nutrients like zinc, antioxidants, and nutritional anti-inflammatories like curcumin and Omega-3 fatty acids, through food or in supplement form.

Bone broth is an excellent restorative for the GI mucosa. As is colostrum.

Repair relates to the 'nutrient-dense diet' element of the Microbiome Protocol.


Rebalance refers to the implementation of systemic restorative processes that will support gut health in the long-term.

These are the powerful lifestyle factors that can get neglected when we focus exclusively food and supplements, like sleep, physical activity and stress management practices (yoga, meditation & mindfulness) which are core elements of the Microbiome Protocol.

Putting the 5 'Rs' into Action

Matthew started a new 3-month treatment this week to address the debilitating nausea that is not responding to dietary treatment.

The current hypothesis is that he has biofilm-protected yeast colonies in his gut.

Yeast can grow roots, called hypha, which puncture the intestinal wall and perpetuate intestinal permeability. Therefore, until these armoured yeast colonies are banished, all of his other efforts at removal, replacement, reinoculation, repair and rebalancing can't fully heal his gut.

Here's how his current treatment lines up with the 5 'Rs':

Remove: This treatment targets removal of the biofilms with a plant chemical called Biocidin and removal of the yeast with Fluconazole, a pharmaceutical treatment available by prescription. Fluconazole needs to monitored with regular bloodwork due to its toxicity.

These removal strategies are in addition to the removal of every possible food, chemical and environmental influence that we know of (& have control over) for the past 20 months, including attempts to eradicate the yeast through diet.

Replace: The treatment plan includes proteolytic enzymes with every meal. Which, for Matthew, has been all of one meal day for many months, due to severe nausea.

Repair: The final element of this new treatment includes a bovine colostrum gut healing.

Reinoculate: Matthew has trouble tolerating fermented foods, probiotic supplements and resistant starches, but if the current treatment is effective and his gut heals, he should begin to tolerate dietary reinoculation. If not, his functional medicine doctor has suggested a trip to the Taymount Clinic in England for a Fecal Microbiota Transplant.

Rebalance: Matthew will continue with all his rebalancing practices, which are now his entire life.

Featured Resource

Fearless Fermentation

Reinoculate with fermented foods. Fearless Fermentation is a video-based fermentation 101 program with Sarah Ramsden, Nutritionist.

Sarah was diagnosed with a brain tumour and multiple sclerosis in the same week. She committed to a healing protocol lifestyle, including Fearless Fermentation and now lives a vibrant life.

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