Q: What do you do when your previously gentle and intelligent spouse starts to behave like a hostile toddler most of the time?
A: Do everything you can to reduce their brain fog!
When his brain fog was at its worst, Matthew reminded me a lot of a hostile toddler.
A hostile toddler with a driver’s license and credit cards.
It was not good!
The brain fog that accompanied the overall decline in his health was one of the scariest symptoms he experienced. And it is one of the many symptoms that has responded exceptionally well to the Autoimmune Protocol (AIP).
We first noticed marked improvement in Matthew’s cognitive function after seven months on the AIP.
And every month it has improved further.
After 27 months on the AIP, he’s almost all of the way back to his smart old self. Not completely. There’s still room for recovery, but his brain has mended remarkably well.
I am fascinated about brain fog, after having watched Matthew descend into its depths and come out the other side. Rory Linehan from the Paleo PI shares my interest, having been ‘there and back again’ with brain fog himself. So, he and and I conducted some research into the phenomenon.
In January 2016, we surveyed 18 people with first-hand experience with brain fog, all of whom were on a healing protocol diet, like the AIP.
This post contains the results of that research.
Our Brain Fog Research
We found it interesting that though they had no contact with each other while our research was being conducted, the way that people described their experience with brain fog was quite similar: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.
All of these protocols are based on the same science and are fundamentally aligned. They are all gut-healing, anti-inflammatory, ancestral eating systems.
This is a big subject, but in short, healing protocols (like the AIP & Wahls) tend to be be more restrictive than the optimization protocols (like Primal & Bulletproof), but then they are elimination diets, with the assumption that some off-limits foods may be reintroduced in time. Whereas, though both Primal & Bulletproof make allowances for more dietary flexibility, optimizers recommend this pattern of eating as a lifelong commitment to peak performance.
So, it’s kind of like this:
Chris Kresser considers sleep to be one of the 9 steps to perfect health.
What follows are selected quotes from a paper that was published in the January 2015 issue of Arthitis & Rheumatology, called Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease by Dr Jose Scher and 13 other researchers.
This study adds additional scientific research to the mounting anecdotal evidence that Autoimmune Protocol pioneers have been amassing, regarding the connection between gut health and autoimmune. It begins to explore the unique constellations of intestinal bacteria that are associated with different forms of autoimmune disease.
This particular paper focuses on Psoriatic Arthritis (PsA) and Psoriasis, two of the interrelated autoimmune conditions that Matthew lives with.
In our ongoing quest to hack Matthew’s health, we constantly seek new information to inform, confirm or disconfirm our observations, hunches & hypotheses. This paper confirms everything we’ve learned through our biohacking to date. It has raised some new research questions for us & could potentially revolutionize standard medical practice for treating autoimmune.
People with Psoriatic Arthritis (PsA) have less diversity in the population of organisms in their gut than healthy people, and they lack particular types of of bacteria: specifically, Akkermansia and Ruminococcus.
People with psoriasis also have reduced diversity in their intestinal microbiome, and the reduction follows a pattern, with maximum variety in healthy people, reduced flora in people with psoriasis alone, and even further reduced diversity in people who, like Matthew, have psoriasis and Psoriatic Arthritis.
In the words of Dr Scher et al:
“In this study…we have shown, for the first time, that patients with PsA and patients with psoriasis of the skin have decreased diversity in their gut microbiota, mainly due to the lower relative abundance of several taxa.”
In addition to less diverse intestinal flora, researchers have identified a “common gut microbiota signature in patients with psoriasis and patients with PsA.”
“Our studies constitute a novel and comprehensive approach to investigate the symbiotic relationship between gut microbiota and PsA. We have identified several organisms that are virtually absent from PsA patients (i.e., Akkermansia and Ruminococcus).”
“The gut microbiota profile in patients with psoriasis appears to be intermediate, between that of PsA patients and that of healthy subjects, suggesting that there exists a possible continuum in disappearing intestinal taxa through the natural history of the disease.”
A “key question left unanswered by our study is whether patients with current psoriasis of the skin alone will lose certain potentially protective taxa, such as Akkermansia and Ruminococcus, at the time of, or prior to, transition into PsA. This is crucial because, although it is established that 25-30% of patients with psoriasis will develop arthritis over time, there is currently no possible way to predict progression.”
Similar research has previously focused on the constellations of gut flora in people with rheumatoid arthritis. A comparable lack of diversity was found, but with a different signature. “We have previously utilized this same approach to examine the intestinal microbiome in treatment-naive patients with new-onset rheumatoid arthritis (RA) and found that expansion of Prevotella copri was associated with enhanced susceptibility to as yet untreated human RA. This is contrast with our present findings in PsA patients and suggests that there is a distinctive pattern associated with each condition.”
Potential Treatment & Further Study
“These investigations may ultimately lead to novel diagnostic tests and interventions, in the form of probiotics, prebiotics, specific microbiome-derived metabolites or molecular targets, and even bacterial transplant techniques.”
“The role of the gut microbiome in the continuum of psoriasis-PsA parthenogenesis and the associated immune response merits further study.”
What if replacing the missing Akkermansia and Ruminococcus could assist in reversing Psoriatic Arthritis? This would likely not be as simple as repopulating the gut with these bacteria. Favorable gut conditions would probably need to be cultivated to allow these extinct organisms to thrive. And re-population might need to be done through ‘bacterial transplant techniques’ including, perhaps, fecal transplants.
We think these findings could revolutionize medical treatment for autoimmune arthritis (and autoimmune conditions generally).
Find the full Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis paper here.
They made candy in Northern England and when they came to Canada, they kept making candy.
There is still a Sweet Shop here in Victoria that was started my forebears.
As an aside, my grandfather wasn’t allowed into his candy-making grandparents’ house, because his mother, Bertha Bland (what a wonderfully unfortunate name), had been a factory-worker in the old country.
And they were lofty candy-makers.
So my grandfather, young Kenneth George, was only permitted on his grandparent’s front porch, whereas the other grandchildren could come & go into the house as they pleased.
My ancestors brought their classism & their candy with them.
That’s how I come to be from candy-land.
Or biscuit land.
Just ponder what all those biscuits are doing to people internally.
Another of my ancestors was a King of Scotland. Sort of a wimpy king, if you’ve ever watched Braveheart: Robert the Bruce.
But all this rambling about British stodge has a point.
The point is I’m descended from candy-making, biscuit-consuming, classist, wimpy colonists.
The health of their intestinal flora can’t have been great, even way back when they were colonizing this great land, and this thought has lead me to wonder about gut health & colonialism.
When all those biscuit eaters with their disorderly intestinal flora and associated nervous complaints arrived here, what did they find?
People eating a perfect paleo diet who were probably enjoying magnificent gut health. If all the research (and my own experience) about the correlation between mental health & gut health is to be believed, Indigenous people were probably also enjoying psychological well-being.
All these happy people. How dare they?
Have another biscuit.
We really need to do something.
And that something was done.
The irony was not lost on me as I drove to work one morning last week, having had bison liver and an avocado and a smoothie made from dandelion greens for breakfast, and I saw three Indigenous kids walking to school with lollipops in their mouths.
The candy makers were thorough.
Just one more reason I am continuing my experiment in nutritional ethics on the Wahls Paleo Plus.