The Six Pillars of the Ancestral Autoimmune Protocol

//The Six Pillars of the Ancestral Autoimmune Protocol

The Six Pillars of the Ancestral Autoimmune Protocol


Every Journey Begins with a Single Step…

When you are on a journey to resolve a complex, multi-system, and chronic illness, how to get the most out of each aspect of your lifestyle matters a great deal.

This article is going to focus on six common sense aspects of day-to-day life that can be combined to encourage more rapid and consistent results. These Six Pillars are the foundation of each of the Four Phases of the Ancestral Autoimmune Protocol. I will come back to the pillars in a moment. First, I want to give you a quick tour of the Four Phases.

The Four Phases:

          • Rest and Recover
          • Reset and Rebuild
          • Restore and Realign
          • Rebalance and Reawaken

As a clinician, I am always looking for ways to augment and improve the protocols that I recommend for my patients. At present, when working with chronic and/or autoimmune disease, or supporting people through the process of resolving trauma or addiction, I always begin with inflammation.

Inflammation needs to be reduced (in most cases) and then modulated properly for tissue repair and growth to be optimal. During this first phase, it is best to rest for a week or two and allow every part of your body and being to recover.

Once your immune system and metabolism have reset and settled down, it is time to repair and rebuild all of your membranes, connective tissues, muscles, nerves, brain, and bones. Your body needs several nutrient and tissue surpluses to heal in this way. When you are ready, your muscles need to be active and toned to keep your Human Growth Hormone (HGH) elevated for this phase to work properly and completely.

Now that your immune system is focused on tissue repair, the third phase focuses on restoring your nutrient stores and to realign your relationship with your vitality and what your future diet and lifestyle will need to be like to keep you healthy and improve your fitness, both mentally and physically.

The final phase supports your long-term health by helping you find an optimal and balanced diet and lifestyle for the long term. This phase also encourages you to reawaken your inner relationship with the deeper parts of yourself that got you through the challenges of your healing journey.

Some people go through the Four Phases in order over a few months, while others need to go back and forth between these phases over a couple of years. Regardless of the phase you are in and how long that needs to take, you are relying on your Six Pillars of health to support you on your healing journey.

Your Six Pillars:

          • Good Food and Nutrition
          • Metabolic Adaptability
          • Physical fitness
          • Mindfulness and Mindset
          • Supplementation
          • Support and Spirituality

Your First Pillar ~ Good Food and Nutrition

Good food is essential because it reminds us that it is worth the time and energy to stay on top of all of the shopping and cooking. For me, good food means that I can’t wait to shop for some fresh ingredients, get home, make a delicious and nutritious meal. And then enjoy every bite. I want to ensure that I am actually solving a problem in the sense of my health. But more importantly, I want to be happy that I can also eat some really good and familiar food.

I’m lucky. I live in a small town with a lot of healthy restaurants, so it is not hard to find good food when I go out. Depending on where you live, it might take you a few weeks to find really good food when eating out. Sometimes you need to get picky with the restaurant staff about what is in the salad dressing and what oils they cook with.

Becoming ‘one of those people’ who have specific food requirements is a part of the dance of resolving an autoimmune condition.  It may feel awkward, but it is absolutely worth the inconvenience or embarrassment.

Good food is a relationship, and a good relationship has a date night. It really depends on what you bring to the date. If you are full of passion and curiosity and playfulness, it is going to be a good date. If you’re there with a bunch of math, it will be that kind of a date – which feels more like a meeting trying to control the bottom line.

I encourage you to make this relationship about good food, not just good math.

I have done all of the math and will explain it in detail in future articles. For now, focus on imagining all of the amazing date nights and delicious meals you will create for yourself and those along for the adventure.

Nutrition ~ Four Phases at a Glance

Your Second Pillar ~ Metabolic Adaptability

Many people who experience a lot of stress and eat a processed food diet have metabolic issues. Their Cortisol levels are too high or low. They have a hard time regulating their Insulin, Glucose, and Triglyceride levels and do not sleep very deeply. Most adults who are not actively working on their health are overweight or obese and have (or will have) a 50% chance of needing pharmaceutical intervention.

The Fat loss industry is one of the biggest business in modern history!

Your metabolism also includes your liver, digestion and elimination organs. If you are not supporting these essential organs and systems on a regular basis, they will begin to limit how healthy you can be and will eventually decide what kind of illness you will have to recover from.

As the saying goes, ‘An ounce of preventions is worth a pound of cure.’

Another word for health and how you will experience the aging process is adaptability. The more resilient and adaptable your metabolism is, the sooner you will bounce back from whatever ails you. The most effective way to improve your metabolism’s adaptability is to change things up and challenge the status quo.

In the 21st century, this looks like fasting, low carb and Ketogenic diets.

Your metabolism also needs to have times of focusing on your Adaptive Resources. Habits like conscious resting, sleep hygiene, acupuncture, massage, and things that your mind and body reconnect and focus on repair are essential. Especially at the beginning.

The most efficient way to make this endeavor more effective is to get some Functional Lab Testing done. This helps you and your support team choose the best supplements and decide how long each of your personal Four Phases needs to be.

Metabolism ~ Four Phases at a Glance

Your Third Pillar ~ Physical Fitness

Your ability to thoroughly heal your metabolism and your capacity to repair every tissue in your body is limited by your level of fitness. I am saying that, not only as a doctor but as an athlete who has spent over two decades helping train other athletes.

When the time is right, improving your fitness in whatever way you choose is going to be crucial. For some people, walking for 30 minutes a day is a good start. For others, going to a fitness class is the only way to gain some momentum and make fitness a regular part of their life.

As I mentioned above, your muscles need to be active and toned to keep your HGH Human Growth Hormone elevated. A sad but important fact is that people lose 10 percent of their metabolic rate and rapidly lose their innate HGH production every decade after 40 years of age.

To get the most out of your pillar of fitness, you will need to go through a few stages. Fitness can look like a person lifting weights or running a long way, but both of those endeavours depend on the health of your mitochondria, the integrity of your connective tissue and fascial membranes, as well as how efficient the messages from your brain get to each individual muscle fibre.

If you are recovering from a long illness and feel up to some exercise, I always recommend some resistance training that gently challenges every part of your body. As your metabolism and muscle cells heal, then it is time to stretch out all of your fascia. Your body is more than what you can make it do. It also has a memory of previous injuries and/or sitting all day. Activating your mitochondria and improving the integrity of your posture and fascia is the same as rebuilding a house or a car from the inside out.

Then it is time to get stronger, and/or more explosive, and/or develop more endurance. Each of these attributes requires that your Central Nervous System develop a new range of capabilities or Adaptive Resources.

Fitness ~ Four Phases at a Glance

Your Fourth Pillar ~ Mindfulness and Mindset

“Mindfulness is how a Mindset works.”

Trying to have a better mindset without having the mindfulness to be aware of your default mindset is not very effective.

Most conversations about mindset focus on getting your goals and long term plans clear. That is a very important conversation to have. Every day, I have conversations about all of the resources, activities, and strategies you will need to create the most adaptable, playful and committed mindset and create the best future possible.

If you are ready to have that conversation, find a coach.

Some of us are not ready for that conversation, though.

When you are going on a long-term clinical journey that may require months or even years of dedication, your mindset will be focused on changing your habits. Or realizing you cannot change some of those habits on your own.

Becoming mindful of who is going on and guiding the journey is absolutely necessary. Changing physiological patterns sometimes includes changing your embodied reactions to stress, impatience, fatigue, childhood trauma and other forms of trauma. At least 30 percent of us are living with some form of addiction as well. When life feels like a non-stop reaction, your mindset becomes reactive.

In my experience, a regular mindfulness practice is the most adaptive, coherent, and life-changing attribute to develop. Changing your life is really about learning to rely on yourself in new ways.

Your mindset will improve the more it includes mindfulness.

Mindfulness ~ Four Phases at a Glance

Your Fifth Pillar ~ Supplementation

The modern food supply is becoming nutrient depleted because our agricultural practices are exhausting the soil. I am not one to focus on the negatives, but this conversation is about your adaptability and your resourcefulness. If you are going to heal your body, metabolism, immune system and your authentic self, then you need to have all of your nutrients in abundance.

Ideally, an organic and seasonal diet will keep most people healthy. If you are trying restore your vitality, win a competition, or live for an extra 20 years, then supplementation is on the menu.

Having said that, I encourage all of my patients to make a clear distinction between general metabolic and tissue support and using supplements to correct a known clinical illness. Lab testing is the only way to certain that you know what you need, why you need it and how long it should take to restore your health.

I always ask new patients to bring in ‘whatever’ they have been taking so we can make some precise and tactical choices. You would be amazed at how many people come into my office with a suitcase full of supplements, wondering why all of that effort and money isn’t working.

Most supplements are essentially concentrated food. They gt used making up for a poor diet. Once people are on a focused and nutrient-dense protocol, it gets a lot easier to make the right choices and get some tangible results.

Each phase of the A-AIP can be augmented by or may depend on the right combination of nutritional supplementation. (See Below)

Supplementation~ Four Phases at a Glance

Your Sixth Pillar ~ Support and Spiritual Practice

If you have ever looked into blue zones, those places in the world where people are more likely live over 100, you will be aware of the many theories that scientists have for why those people live so long.

In a recent global study of these regions, there is finally a consensus on what is making these people so healthy and have such longevity. Although they eat well in different ways, they are fit, and they spend a lot of time outside, the one thing that they all do is they have good connection and support. They share meals – healthy or not. They connect and talk to each other and collaborate in meaningful ways at any time of day.

Who would have guessed?

If you have a chronic illness, or if you just want to live a long time, connection is the world champion for better health outcomes and longer lives.

Being met in the places where you are physiologically, mentally, emotionally, or perhaps energetically is one of the hardest thing any of us will ever do. It takes a combination of courage and vulnerability to ask other people to support you while you work out your past and arrive in your life in a more conscious and committed way.

As a clinician who works with complex conditions, I have become aware that I often meet people when they are facing the hardest time in thier lives.

Spirituality is a very personal part of life. So is suffering with life-altering symptoms that affect you every day.

Most Spiritual traditions encourage some form of regular practice. Meditation, Yoga, and Qi Gong are taught in every city in the world because it is an instinct to soothe yourself and reflect on your experiences. If your life is more of a challenge than a ceremony, if you need support and solace, find a daily practice.

I will sharing more about Qi Gong and meditation soon.

As a clinician, and as a patient, I am also excited to be a part of the integration of psychedelic compounds and entheogenic plants into the ttreatment of PTSD, Addiction, and Depression. Almost all of these substances are known because of their use in the oldest Spiritual traditions in the world.

If you a person who relies on prayer, then make every step a prayer!

If you think all of this spiritual stuff is full of crap, focus on gratitude. We can all find something to be grateful for.

Support and Spirituality ~ Four Phases at a Glance

How are Your Six Pillars?

I hope that basic outline gives you a place to start. The next time you need to improve your health or prepare for a competition, sit down and design a Six Pillar Protocol for yourself.

What would the best (and most enjoyable) diet need to be?

Which systems and organs that make up your metabolism need the most time and attention?

What kind of fitness challenge or how long of an exercise break do you need right now?

Have you ever committed a few weeks to a mindfulness practice and how can you improve your mindset?

If you are taking a handful of supplements every day, are you sure that they are optimized for your health and your goals?

Do you have the support you need from those around you and the authentic Being within you?


Michael Smith is an internationally respected Clinician, Author, and Speaker. Michael practices Functional Medicine, Acupuncture, Traditional Chinese Medicine, and encourages his patients to follow an Ancestral approach to lifestyle and diet. Dr. Smith has dedicated 25 years to the research and treatment of Chronic Illness and Autoimmune Disease. As an Autoimmune patient, Michael is intimately aware of the devastating impact these conditions can have on your quality of life.

Dr. Smith is also at the leading edge of the treatment strategies, dietary protocols, and the precise lab testing needed to resolve these complex conditions. 

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