Like the microbes in our gut, the microflora that live on our skin defend their habitat for their own survival, and depending on whether the resident communities of microbes are ‘commensals’ (our allies) or pathogens, these residents either offer us protection or cause us harm. Read More
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:
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.
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.
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 (in 3 forms: drops/advanced formula, capsules & throat spray) 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 product called GI Restore from NuMedica for gut healing.
Reinonculate: Matthew is unable to tolerate any fermented foods, probiotic supplements or 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~.
Part one of this post looked at stress management, diet, sleep and physical activity.
In this post we’ll survey the other elements of the microbiome protocol:
Gut health therapies.
Starting with a sneaky one:
Chris Kresser cites research about the benefits of coffee in this podcast and sums up that “it still might be harmful for an individual based on a number of different factors”.
Sarah Ballantyne considers the research in the Pros & Cons of Coffee including the health benefits and it’s effect on cortisol production. She summarizes: “if you are very healthy, have lost most of the weight you need to lose, have regulated your hormones and healed your gut, coffee (in moderation) is likely to provide you a health benefit.”
Dave Asprey, the originator of Bulletproof Coffee, is a advocate of daily low-toxin coffee.
Back in 2008, Mark Sisson cited research on the negative impacts of caffeine and echoes Chris when he asks: “Is it really just a pick-me-up, or is it a band-aid for a larger problem like sleep deprivation, hormonal imbalance, lack of physical activity, lack of adequate sunlight?”
And there’s chlorine in our water, which indiscriminately kills bacteria, including many of the friendly microbes we’re trying to nurture inside the gut. Chlorine is flagged by David Perlmutter in Brain Maker (he recommends simple water filtration as a solution). It’s also addressed by Josh Harkinson in this Mother Jones article.
Epigenetics is the study of how the expression of our genes is affected by our environment.
We get issued our genes at conception, but our environment is more within our control.
The environment is exactly what this microbiome protocol is designed to address.
Terry Wahls reminds us that “diet is the most powerful epigenetic factor of all” and goes on to list toxic chemicals, physical activity level, stress, relationships, sleep, and the microbiome itself as other elements of our environment that turn our genes (for health & disease) on and off.
This 2007 documentary on epigenetics is also excellent~.
Gut Health Therapies
All of the elements in this microbiome protocol are gut health therapies.
But additional interventions specifically target the health of the microbiome, including relatively simple approaches like inclusion of resistant starch, fermented foods & probiotics in the diet, and more radical interventions like Fecal Microbiota Transplants.
New research is surfacing almost every day. Some of it I don’t fully comprehend.
Most recently, I’ve been reading David Perlmutter’s Brain Maker, which simplifies things enormously.
Here’s a step-by-step (with diagrams~) of my current understanding of the origin of illness. As ever, I welcome your thoughts.
The Origin of Illness
Both health and illness begin in the microbiome.
Here’s the basic idea:
My initial understanding involved a 3-step process:
Inflammatory food upsets the balance of the bacteria in the gut, resulting in intestinal permeability.
This allows foreign particles to leak into the body, causing systemic inflammation.
Inflammation causes disease.
The connection between diet and gut health is the foundation of the nutritional elements of the Autoimmune Protocol as outlined in The Paleo Approach by Sarah Ballantyne, (as well as all other evidence-based healing protocols like the The Wahls Protocol and The Bulletproof Diet).
But not only autoimmune conditions are caused by an unhealthy imbalance in the microbiome: it seems that most illnesses are.
The notion that most chronic health conditions are at least partly caused by inflammation is, in itself, a radical departure from the previous, mechanistic understanding of health. But this story gets way more interesting:
Inflammation isn’t the only cause of health problems.
We also need to consider genes & environment. Which leads us to…
Epigenetics is the study of the interaction between genes & environment. It’s partly this interplay that determines whether or not a genetic predisposition to a particular disease gets activated in response to systemic inflammation.
And helps explain why one person might get Psoriasis while another one gets Multiple Sclerosis.
Here’s a cute overview on Epigenetics:
The Origin of Gut Dysbiosis
Gut dysbiosis is an unhealthy imbalance in the microbiome and as mentioned, it is this imbalance that is a primary culprit in illness.
What causes an imbalance?
In addition to an unhealthy diet, chemicals (like chlorine); environmental factors (like excessive hygiene); side effects from drugs (including antibiotics); Caesarean birth and formula or bottle feeding all contribute to dysbiosis.
Before we are born, we have a minimal microbiome. We begin to acquire a robust one at birth. A vaginal birth followed by breastfeeding is the best possible way to get a healthy and protective microbiome started.
Interestingly, Dr Natasha Campbell-McBride suggests that a newborn receives microbiota from both the mother and the father (or the mother’s other sexual partners) during vaginal delivery. Which gives a whole new meaning to the term ‘dirty sex’~!
Stress is a really big deal.
Not only does ongoing stress contribute to gut dysbiosis through elevated cortisol levels, but gut dysbiosis causes stress.
And because chronically elevated cortisol levels contribute directly to intestinal permeability and inflammation, stress creates a nasty reinforcing loop of disease-provoking conditions in the body.
What causes stress?
We just weren’t designed for living this way.
Toxins in the Brain
We used to think that the blood-brain barrier protected the brain from toxins. According to David Perlmutter in Brain Maker, that isn’t so.
Intestinal permeability allows toxins into the body and some of these travel up to the brain.
This is one explanation for the mental health epidemic we are now experiencing, including widespread depression and anxiety.
Remarkably, toxins can stress the brain into perceiving threat, which automatically triggers a neurological takeover by the limbic system.
The limbic system does a great job of protecting us from old-school hazards like predators, but is incapable of higher reasoning or anything approaching enlightenment, and simply can’t navigate the complexity of modern life.
So these toxins not only provoke depression and anxiety, but can render us incapable of making good decisions.
The Collateral Damage of Chronic Health Conditions
Compounding the problem, people who end up with chronic health conditions end up dealing with a host of other factors that contribute to stress, including pain, financial impacts and negative effects on relationships, which add add to the stress fest that help create their illness in the first place.
Obviously, the presence of toxins in the brain isn’t the only cause of mental health issues. The whole point of creating a convoluted spaghetti diagram like this one is that the origin of illness is complex.
In addition to epigenetics (genes & environment), trauma & brain architecture are significant factors to consider when thinking about our mental health.
I haven’t seen any reference to the connection between microbiome research and neurological development research in the literature, but it’s highly relevant.
(Still with me? We’re almost done~!)
Toxic Stress & Brain Architecture
Neurological research over the past 20 years has demonstrated that toxic stress in childhood changes the architecture of the brain.
The basic idea is that all children experience stress, but prolonged stress without the support of a caring adult is toxic to early brain development and permanently impairs executive functioning.
The ability to handle stress, fascinatingly, is wired into the same part of the brain as executive function skills, so that reduced executive function capacity also results in reduced ability to handle stress throughout the lifespan.
Executive function skills are also exactly what become impaired in an adult who experiences brain fog as a symptom of systemic inflammation.
Trauma & Nervous System Dysregulation
Finally, trauma, whether it occurs during childhood or adulthood, can result in nervous system dysregulation, which also impairs the body’s ability to manage stress.
So there it is.
My current (& no doubt flawed & incomplete) understanding of the origin of illness.