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~.
I had read Sally Fallon Morell’s Nourishing Broth, and I was convinced about the benefits of marrow.
“Deep in the centre of bones is marrow, a creamy substance valued by our ancestors for it’s life-giving, reproduction-enhancing, and brain-building fat and cholesterol. As the seedbed of blood and stem cells, it’s prized as a sacred, energizing and regenerative food in native cultures all over the world.” Sally Fallon Morell~
My #1 kid loves marrow. She eats it with a spoon.
Matthew adores it, too.
After we make a batch of bone broth (which is every couple of days, thank you Instant Pot!) he slurps the marrow right out of the bones.
I still haven’t found the strategy for kidney, I admit.
My Bone Marrow Strategy
My first attempt at eating marrow was to scoop it into the container of bone broth. That way I’d consume it by default.
But I was still feeling squeamy about it, so I knew my strategy needed work.
I started to blend it with the bone broth before storing it in the fridge.
And then I began to use that rich gravy-like broth, hot, for dipping, au jus style.
From the first bite, I knew I’d found my bone marrow sweet spot.
Au Jus & Pot Roast
(Au jus, by the way, is pronounced Oh-zhoo~).
For the pot roast, you can use a tough cut from any ruminant: beef, lamb, bison, vension or elk.
The tougher the better.
For a cow, that’d be a chuck, brisket or bottom round roast.
But here’s the roast selection strategy I use: when I’m at my butcher (which only sources pastured meat, so I don’t need to worry about that criteria), I just pick the cheapest one.
And the last time we got half a cow from Ruby Slipper Ranch (which was just this week, thank you Tracy & Shayne!) we asked for more roasts and less ground beef. So we can eat Pot Roast with Bone Marrow Au Jus all fall…
Pot Roast with Bone Marrow Au Jus
This recipe takes almost no time at all over 2-3 days. You can do it in one day if you are one of those crazy cats who has an Instant Pot and a slow cooker (and you already have some bone broth ready~).
If you are starting from scratch, you first need to make some bone broth. I’m including a slow cooker recipe here (you can find Matthew’s Instant Pot Bone Broth recipe below and Eileen’s Instant Pot recipe here).
Then you need to cook your pot roast, which takes a day (or a night) in a slow cooker.
Slow Cooker Bone Broth
5 lbs marrow bones, ideally with some meat still on them
1/4 cup Apple Cider Vinegar
2 Bay Leaves, optional
Brown the bones in a 350 degree oven for 30 minutes, turning them once or twice.
Place them in the slow cooker, cover with filtered Water, add the Vinegar and the Bay Leaves (if using).
Cook on low for 24 hours.
The stock should barely simmer. If it’s too hot, adjust the lid to cool everything down until the bubbles are just barely breaking the surface. Replace the water that evaporates, as required.
Remove the marrow bones with a slotted spoon. Once cool, scoop out the marrow from each bone with a knife and put it in a glass container. Cover with 1 cup of bone broth and refrigerate.
Refrigerate the rest of the bone broth in a separate glass container.
1 4-5 lb pot roast
Himalayan Salt (or similar)
2 tablespoons tallow or lard
3 cups bone broth
Generously Salt the Roast.
Heat the fat in a skillet on medium-high heat and brown the roast on all sides.
Place the roast in the slow cooker.
Deglaze the pan with the bone broth, scraping any meaty bits up and pour it over the waiting Roast.
Turn it to low and walk away fro 7-8 hours (if it’s a little longer: no harm done).
Refrigerated bone marrow in bone broth
Bone broth from cooking the Pot Roast
1 teaspoon Savory
1 teaspoon Marjarom
Once cooked, let the Pot Roast rest while you heat the chilled bone marrow in bone broth with the extra-meaty broth from the slow cooker. Add the Herbs.
When piping hot, puree in a food processor. Serve immediately as a dipping sauce for the Pot Roast.
Matthew's Instant Pot Bone Broth
Matthew makes Bone Broth every 3-4 days, as he consumes 2-3 cups a day as part of his gut healing protocol. Here’s his recipe:
5 lbs marrow & cartilage-rich bones, ideally with some meat still on them
1/4 cup Apple Cider Vinegar
Preheat the oven to 350.
Brown the bones for 20 minutes, before turning them, switching on the broiler to 400 and broiling for an additional 10 minutes.
Place the bones in the Instant Pot.
Add water to 1/4″ below the maximum capacity line.
Add 1/4 cup of Apple Cider Vinegar.
Press ‘SOUP’ and adjust the timer to 120 minutes.
Allow 40-60 Minutes to pass after that session expires, to depressurize the pot.
Press ‘SOUP’ again and adjust the timer to 90-120 minutes.
Allow at least 20 minutes to pass to partially depressurize the pot.
Turn the pressure switch to ‘VENTING’ and allow all the steam to escape.
Optional: Press ‘SLOW COOK’ and set timer for an additional 4-5 hours.
Strain broth through a colander. Remove & consume all the marrow from the bones.
Slowly, I’m recovering for my decades of vegetarianism.
Nowadays I can have a venison pot roast cooking inside, while contemplating the possibility of future venison pot roasts outside~.
We all want to be healed, and so we look for confirmation that healing is possible, holding on to the narratives of miracle-cures and magical-remissions like talismans for our future well-being.
But the reality is that healing autoimmune is slow, non-linear and perhaps always incomplete.
Once a body is in autoimmune response, it is always in autoimmune response.
And if we don’t get that at first, it can lead to disillusionment and an unwarranted sense of failure.
In truth, most of the autoimmune bloggers that I know experience flares, even after strict commitment to the AIP for years. Many of them write about their setbacks on their blogs or social media. Some don’t.
Tara Perillo from Paleo Cajun Lady says “I always share my ups and downs in blog posts and social media. I feel like people are coming to us for the truth, not some perfect AIP fantasy land. I do try to end each negative post with a positive message, however. People appreciate that even we struggle.”
Susan Vennerholm from Backcountry Paleo agrees: “I feel that sharing the ups and downs of living with AI is important. We’re not superheros, and I think when readers realize we all have challenges, it makes the journey feel that much more doable. The important message is that even with these setbacks, we keep at it.”
Other bloggers choose not to share information about their health challenges, for various reasons, including that it can create vulnerability during a time when they don’t have the strength to deal with critical comments (or lack of response) from readers.
As Rory Linehan from the Paleo PI explains, “I try to focus on the positive but mostly, when I’m going through a setback I don’t want to share it until I’m out the other end and I can gain some sort of insight on it. Then by the time I’m out the other end, things are rosy again. I’m conscious that I’d like to share more of the challenging aspects of dealing with chronic illness, it’s just I want to frame it in a positive and not a negative light – which is challenging.”
Emma King from The Bacon Mum elaborates “It’s really important to share, but when I was at my worst this year and in a flare I just couldn’t cope emotionally with any negative responses to my posts.”
Dora Siah from Provincial Paleo explains, “Sometimes people just want to read the positive aspects to affirm that they’re doing the right thing. Especially the ones that feel defeated easily. Other times you get people wanting to hear about the difficulties others face, so as not to feel so lonely in their healing journey.”
Eileen Laird from Phoenix Helix points out “Many bloggers do share their setbacks, but that doesn’t mean people find those posts. We tend to find what we are looking for, which is why when I wanted a cure, those are the stories I found.”
In this post I’m sharing a web-log of posts that get into some of the challenges faced by people who are healing through diet and lifestyle.
So we can look reality in the eye, while still maintaining our faith in healing (that’s the Stockdale Paradox~).
With tremendous respect (& gratitude) for the honesty, here they are:
The Difference between Reversing Autoimmune Disease and a Cure by Eileen at Phoenix Helix. “As my two-year healing diet anniversary approached, something surprising happened. Instead of feeling grateful, I would find myself crying for no reason, carrying a sadness I didn’t understand. It took me a while to realize it was a deep grief over not being cured.”
On Finding What Works by Emily at Field Notes on Healing. “I had to face the fact that a year using the autoimmune protocol (AIP) diet, lifestyle changes, and functional medicine (along with the medication my doctor had prescribed me) were not enough to fully correct my rheumatoid arthritis symptoms.”
Endometriosis Surgery by Angie at Autoimmue Paleo. “I would be a liar if I said there is no part of me that isn’t having a little bit of a pity-party. I have worked tirelessly for two & half years following Autoimmune Protocol & adopting Paleo lifestyle changes. Those things dramatically improved my health & I had hoped they were enough to manage Endo. They are not.”
Bending Not Breaking: My consent to surgery by Martine at Eat Heal Thrive. “I had to confront the reality in my very-much-ongoing healing journey that no amount of medication, clean eating, and stress management could address this current complication.”
My Personal Battles with Stress by Sarah at The Paleo Mom. “The truth is that the last year and a half have been super tough for me healthwise. I have really struggled with both my physical and emotional health as the result of high stress. Primarily, my complaints have been gaining weight, fatigue, joint pain and some tendonitis, mild depression, and active lichen planus lesions.”
An interview with Terry Wahls by Eileen at Phoenix Helix. “It takes a long time for your body to repair damage that took 35 years to develop. It might take 10 years to heal that… My stamina is incrementally improving, but I’m certainly not yet at the equivalent stamina of another 57 year old in good health.”
Am I an AIP Failure because I Haven’t Reached Full Remission? by Tara at Paleo Cajun Lady. “I have completely healed a stomach ulcer, various psoriasis rashes, inflammation in my intestines and colon, butterfly rash, fibroid tumors, bleeding gums, leaky gut, and the list goes on. But, I still have improvements to make. I still have symptoms to deal with.”
Accepting Illness by Christina at A Clean Plate. “When I say I feel amazing, I’m talking about being able to get out of bed, keep up with my household chores, hang out with my boyfriend, and eventually make it back to bed without anything bad happening. More often than not.”
I’ll Never be a Paleo Success Story (and why I’m okay with that) by Jaime at Gutsy by Nature. “The ever present danger for those of us who are using food as part of our healing strategy is that we end up letting an awareness of what we do and don’t eat become an obsession. Where is the line between eating a healthy diet and disordered eating?”
What Does an AI Flare Look Like for Me by Alaena at Grazed and Enthused. “Why am I sharing these personal details of an autoimmune flare with the Internet? Because autoimmune disease can be a lonely place…”
Getting back to my Blogging Roots: An Update on my Life by Katy Haldiman. “During my journey, I have had some setbacks and struggles, which I believe is a common experience among people with autoimmune disease. A return of migraine headaches was one such struggle for me. A frequently drooping eyelid from myasthenia gravis was another.”
To Medicate or Not to Medicate… that is NOT the question by Slightly Lost Girl. “One of the things I often hear in the AIP community is, ‘I am sick, but my diet isn’t working, so I am going to give up and just take my medication instead.’ For me, there is a fundamental flaw in this statement. It is like saying ‘I got hurt in a car accident, so seatbelts obviously don’t work. I am going to just put a cast on my broken leg instead of wearing a seatbelt.'”
Biohacking Update: 17 months on the Autoimmune Protocol. This one’s mine: about the progress of my husband Matthew on the AIP. “After 16 months on the Autoimmune Protocol (AIP), we were back where we’d been at the worst of Matthew’s autoimmune crisis: he was almost completely incapacitated & unable to care for himself. Despite that, the AIP is working.”
Christie’s Story on Phoenix Helix. “I’ve felt close to remission many times in the past year. I have very little psoriasis left on my scalp or torso. Why I get so close and then have a step backwards, I have no idea. I wish I knew. I wish I understood everything my body is trying to tell me.”
In this Healing Stories podcast, Eileen interviews people who have had a variety of healing experiences on the AIP, including Melissa who, at one time, was bedridden for 18 months. As Eileen summarizes, at the time of this podcast, Melissa was “independent in self-care and no longer disabled. She needs to rest after periods of activity, but she has quality of life again. And she’s reduced her medication substantially. At her worst, she took 36 pills a day. Now she’s down to 8.”
Insecurity: What Happens Behind the Scenes by Angie on Autoimmue Paleo. “Even though I… am actively working here to form deep human connections, specifically around the struggle of illness and the journey to health, it is still sometimes really tough for me to be truly open and vulnerable.”
My deep appreciation to Eileen from Phoenix Helix for inspiring me to put together this post and for finding links for me~.
Eileen is reversing Rheumatoid Arthritis on the AIP. Recently she wrote on facebook:
I am not cured. I’ve never met anyone with autoimmune disease who was cured. Nor am I 100% symptom-free. Complete remission is rare with autoimmunity. I have improved my symptoms by 95% through the autoimmune paleo diet and lifestyle, and where I started (excruciating pain and disability) to where I am today (a full and beautiful life) is night and day. But it’s not perfection. In addition to diet and supplements, I take 1 Aleve tablet twice daily to manage my remaining inflammation. For someone with a severe form of RA, that’s amazing, and I’m grateful. It’s the only medication I take. I’ve been honest about this on my blog, but sometimes people miss these details. I’m sharing this today, because I want you to know that if you haven’t achieved perfect healing you aren’t alone. Some people need more medication than I do. Some people need less. Some people regain all of their abilities. Some people regain some. I interview a lot of people for my blog and podcast, and I believe every step forward is cause for celebration: any ability you reclaim, and pain you relieve, any energy you regain. That’s reversing autoimmune disease. It’s not about perfection. It’s about living your best possible 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.
Waking up in the morning to the heavenly smell of bacon.
That you didn’t have to cook.
It’s almost like having one of those mythological ever-happy 1950’s housewives doing magical things in your kitchen while you sleep.
But way less weird.
In the morning, you just throw a handful or two of radishes into the slow cooker while you putter about getting ready. And then sit down for a weekday breakfast that will make every single person you know drool.
Even the vegetarians~.
Preparing this breakfast takes 5 minutes the night before.
Slice the pork belly (re-purpose your old bread knife to slice it up quick). Top & tail the radishes & pop them in a container in the fridge. Then go to sleep.
In the morning, all you have to do is dump the radishes in the slow cooker & turn the heat to high.
Keep in mind, this here is rich. Adding a side of sauerkraut or another fermented vegetable is a nice way to balance out the glorious full-fat intensity.
Heavenly Slow-Cooker Pork Belly with Radish Hash (AIP)
1 lb Pork Belly
1 teaspoon Himalayan Salt (or similar)
2 bunches radishes
Slice the Pork Belly into thicker-than-bacon strips and lay them in the bottom of a slow cooker.
Sprinkle the salt over top.
Put to the lid, set on low and cook for 8-9 hours.
Turn the slow cooker on high while you trim the radishes and cut them in halves & quarters (unless they are very small) and add to the slow cooker.
Give the contents a little stir to coat the radishes in the liquid fat. Replace the lid and cook for another 40 minutes.
Serve with cold raw sauerkraut or sliced cucumber.
Note:You’ll have a lovely bit of rendered lard left in the pot. Pour it in a small glass container and pop it in the fridge~.
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.