Healing From Autoimmunity

Tired of seeing doctor after doctor, and still not feeling better?

Autoimmune diseases have reached pandemic levels in developed nations. 80 million people suffer from autoimmune disease in the U.S., and 150 million suffer worldwide. It’s the third leading cause of death — what do we know about it?

Autoimmunity has a mechanism. It is a somewhat predictable progression of events. With the high mortality rates and increasing number of people who are being diagnosed with one or more autoimmune diseases, combined with the preventative nature of autoimmunity, reducing its prevalence seems to come down to education and putting into practice what research reveals is the key to attaining and maintaining good health.

What is the Mechanism for Autoimmune Diseases?

Step 1: The Birth of Autoimmune Diseases

The birth of autoimmunity starts long before any condition or symptoms appear. It begins at conception. Do you have your mom’s eyes and smile but have more of your dad’s body type? We are not little clones of one of our parents. While your parents pass on traits, your DNA is unique to you. This DNA is your genetic coding that sets you up for life. It is always there, from cradle to grave.  

The question is: Which genes are being expressed, and which genes are “turned off” for the moment?

While in the uterus, the fetus lives in amniotic fluid. This fluid helps protect the baby in a number of ways, including acting as a shock absorber, regulating the baby’s temperature, and passing along antibodies to help it fight infections. Yes, even in the womb, the baby is exposed to things it needs to fight off.

Upon birth, babies have leaky guts that need to close and heal to live outside of its protective amniotic sac. This is why the first few days after delivery, a lactating mother produces a thicker type of milk called colostrum, which turns on the gene to heal the gut.

The gut is not actually healed at that time; the colostrum just turns the gene on and lets the body heal.

Mom continues to pass along a little added immune protection, including white blood cells, antibodies, proteins, and minerals over the next week or so through the colostrum. Little by little, the colostrum is replaced with mother’s milk.

Step 2: Environmental Triggers of Autoimmune Diseases

Now you build upon what genetics you have, and you add in environmental triggers, like dietary components, infections, and toxic chemicals. This is where epigenetics enters. When people ask the question, “Is it nature or nurture?”,  it isn’t an either/or answer. They work together. It is often said that genetics load the gun and epigenetics pulls the trigger. That’s a great way to explain epigenetics, although not an entirely complete picture of the mechanism of autoimmunity at large. The term epigenetics refers to the change in the expression of the genes. Environmental triggers vary from person to person. One person may have heavy metal toxicity, mold toxicity or exposure to EMFs. Another person may have a food sensitivity, an infection, or exposure to contaminated air or water. Yet another may be triggered by a traumatic event, a period of high stress, anxiety, or poor lifestyle choices.
Often discerning which (and how many) triggers are negatively influencing your health is the trickiest part. Testing can take a lot of the guesswork out and potentially eliminate years of frustration. As a first step, you can begin by removing gluten, dairy and sugar from your diet. These are common antigens that wreak inflammation. Many people see symptom improvement with the removal of this terrible trio. Your body is under attack constantly. Our bodies were designed to heal, but they were designed long before plastics and wireless phones and cars. Think of yourself just like an animal found in nature. That’s your environment, too. Anything you can do to reduce the workload your internal system has to fight off will make it easier for your body to support you. I always recommend cleaning up your food and environment from any known toxins — laundry, health and beauty products, foods with pesticides, plastics, aluminum … If it is toxic and you know it, just say no.

Step 3: A Breakdown of Oral Tolerance Leads to Autoimmunity

At some point we cross the line. Let’s take wheat for example. Wheat is a minor toxin. It doesn’t incite a big response. Usually the immune system will say “Wheat? No problem. Let it go. Let it go,” until you cross the line. It’s called “loss of oral tolerance.”

When you have a loss of oral tolerance, oral meaning what you eat, you can’t tolerate it anymore. When you lose oral tolerance and your immune system starts making antibodies to wheat, it starts causing problems in your body systemically.

This can happen when you’re 2 years old, 22 years old, 72 years old, or 92 years old. Loss of oral tolerance can occur at any time. You start making antibodies and molecular mimicry and a slew of other problems. The question: “What causes the loss of oral tolerance?”

Where does loss of oral tolerance come from?

The simple answer is that the loss of oral tolerance is due to all of the toxic chemicals we’re exposed to in our life. Our immune system is fighting Bisphenol A (BPA) that’s in plastic. It’s fighting mercury in tuna fish. It’s fighting PCBs in apples. It’s fighting the pesticides that are sprayed on vegetables. The immune system is fighting all of this stuff all day, every day. It becomes so trigger happy fighting all this stuff that it becomes more sensitive to minor irritants like wheat.

A loss of oral tolerance is the “straw that broke the camel’s back” moment. Once it happens, you make antibodies to the wheat. You have Memory B cells, and you’re toast.
When you have a loss of oral tolerance, your body can no longer distinguish the good from the bad, your tissues from foreign invaders. It is when your body begins to betray itself.

Step 4: A Change in Gut Microbiota Sets You Up for Autoimmunity

Over 70% of your immune system resides in your gut. The microbes in your body outnumber cells by 10 to 1! Diversity in your intestinal tract can help lower the occurrence of autoimmune diseases, allergies and skin conditions. Exposing yourself to a rich collection of microbes through diet and getting your hands dirty, as well as limiting exposure to antimicrobial products, pesticides and chlorinated water can fortify your microbiome and calm your immune system.

When the balance of good and bad bacteria gets thrown off from things like antibiotics or poor diet, dysbiosis occurs. The goal is to always have more of the good guys, so you always want the big army around you to protect you. When you lose some of the good guys, some of the bad guys rear up their ugly heads and start causing problems like leaky gut.

Step 5: Pathogenic Intestinal Permeability: The Gateway to Autoimmune Diseases

At this point, you are fanning the flames of inflammation that already exist. Intestinal permeability (better known as leaky gut) is when your intestines allow objects that have not been broken down to enter the bloodstream (before they are able to be of benefit).

Pathogenic intestinal permeability occurs when this happens over and over again to the point that your gut does not reseal itself naturally. This leaky gut allows large macromolecules to exit and trigger an immune response.

At this point, you may see an increase in the number of foods you become sensitive to because your body is attacking a large number of foods exiting your gut before they should.

Step 6: Immune Reactivity

The stage is all set for autoimmunity. You have your weak links in your genetics. Triggers are firing. Your immune system is weakening, and while it is in this fragile state, you launch foreign objects throughout the body via the bloodstream.

Your immune system has two basic strategies for defense: the innate immune system and the adaptive immune system.

Your innate immune system produces cytokines. These are your first responders in a crisis situation. They identify threats and attempt to destroy them. Cytokines get triggered by foreign invaders like infections, viruses, bacteria, or parasites.

If the threat is overwhelming or ongoing, your innate immune system calls for backup. It brings in the heavy artillery, which is your adaptive immune system, which launches antibodies to attack.

Both of these responses are a fight for survival. The production of antibodies activates a molecular mimicry response and other pathways. The autoimmune mechanism is activated, and you begin to not only make antibodies to destroy an object like food, but your own tissues.

Step 7: Welcome to Autoimmunity

Congratulations — You are now on the autoimmune spectrum. So let’s look at what autoimmune diseases look like.

You pulled and pulled at the chain until you found your FIRST weak link. Let’s bypass all the doctors and tests (and time) that it has taken and go straight to the facts — You have a diagnosis. If that diagnosis is a condition stemming from autoimmunity, a typical doctor will go into symptom management for that specific diagnosis. This is where traditional medicine fails us.

Your diagnosis is a symptom, not the actual problem. If you don’t figure out what the source of the problem is, odds are it’s still happening.

Take Ben’s story for example. Ben is a fictional character, but his story will be familiar to many people with celiac disease, one of many overlooked autoimmune diseases. Unbeknownst to Ben, he has a gluten intolerance.

As a small child, Ben had recurring ear infections. He was treated with antibiotics multiple times that affected his microbiome, thereby putting him at risk for autoimmunity.

A year later, Ben gets sick and seems to be having difficulty breathing. His doctor diagnoses him with asthma. He is given a prescription to help ease respiratory distress while having an asthma attack, and another to help preventatively. Ben can breathe again.

A couple of months later, Ben falls into a deep depression. A psychiatrist prescribes antidepressants to Ben. They seem to help, but he’ll need to remain on them daily for life. Ben seems happier on the meds than off, so he remains on the prescription.

Suddenly, Ben begins to experience an excessive thirst, and he is urinating often throughout the day. He seems to be losing weight, so he returns to his family physician. Ben is diagnosed with Type 1 Diabetes. His pancreas is shutting down, and for the remainder of his life Ben will need to take insulin.

Yet still, Ben remains undiagnosed as celiac, so he continues to fuel inflammation within his body by eating foods containing gluten. No one ever diagnosed the real problem — just a series of symptoms that were initiated by an unaddressed gluten intolerance problem. Meanwhile, the autoimmune diseases just keep coming.

Why Functional Medicine is Superior in Tackling Autoimmune Diseases

Educational Center

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by Dr. Tom O'Bryan
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Autoimmunity & Gluten: What's The Formula?
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Autoimmune Diseases:
Common and Often Overlooked Causes
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The Autoimmune Solution
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Why Women Get More Autoimmune Diseases
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Coriolus Versicolor

Coriolus Versicolor, a remarkable mushroom, is esteemed for its potential to contribute to overall wellness. Known for its immune-supporting properties, Coriolus Versicolor may help strengthen the body’s natural defenses. This extraordinary mushroom has also been associated with promoting healthy energy levels, supporting digestion, and fostering vitality.

Fo Ti

Fo Ti, a revered Chinese herb also known as He Shou Wu, is valued for its potential to support overall wellness. Traditionally used for promoting vitality and longevity, Fo Ti may contribute to maintaining healthy energy levels, cognitive function, and immune system performance. This remarkable herb has also been associated with supporting liver and kidney health, as well as fostering a sense of overall balance


Agave, a versatile desert plant native to the Americas, is recognized for its potential to support overall wellness. Rich in natural fibers and low-glycemic sweeteners, Agave may contribute to maintaining healthy blood sugar levels, digestive health, and providing a natural alternative to refined sugars.

Maral Root

Maral Root, a potent adaptogenic herb native to Siberia, is celebrated for its potential to contribute to overall well-being. Known for helping the body manage stress and maintain balance, Maral Root may also promote healthy energy levels, endurance, and cognitive function. This exceptional herb has been associated with supporting the immune system, fostering vitality, and enhancing physical performance.

  • Antioxidant and DNA Repair Stimulating Effect of Extracts from Transformed and Normal Roots of Rhaponticum carthamoides against Induced Oxidative Stress and DNA Damage in CHO Cells:https://pubmed.ncbi.nlm.nih.gov/27034736/


NotoGinseng, a distinct variety of Panax ginseng native to the Changbai Mountains, is esteemed for its potential to contribute to overall well-being. Renowned for its adaptogenic properties, Noto Ginseng may help the body manage stress and maintain balance. This exceptional herb has been linked to supporting cognitive function, promoting healthy energy levels, and boosting immune system performance.


Baicalin, a potent bioflavonoid derived from the Scutellaria baicalensis plant, is appreciated for its potential to promote overall wellness. With its antioxidant and anti-inflammatory properties, Baicalin may help protect cells from oxidative stress and maintain a balanced response to inflammation. This remarkable compound has been associated with supporting liver health, promoting cardiovascular function, and fostering a sense of vitality.

Purple Lapacho

Purple Lapacho, a unique and potent herb, is valued for its potential to support overall well-being. Known for its immune-boosting properties, Purple Lapacho may help fortify the body’s natural defenses. This remarkable herb has also been associated with promoting healthy energy levels, supporting digestion, and fostering vitality.

Holy Basil

Holy Basil has been found to protect organs and tissues against chemical stress from industrial pollutants and heavy metals, and physical stress from prolonged physical exertion. It has also been shown to counter metabolic stress through normalization of blood glucose, blood pressure and lipid levels.


Ashwagandha, a revered adaptogenic herb, is acclaimed for its potential to support overall well-being. Known for helping the body manage stress and maintain balance, Ashwagandha may also contribute to healthy energy levels and mental clarity. This remarkable herb has been associated with promoting relaxation, supporting the immune system, and fostering vitality.


Guarana, a powerful plant, is celebrated for its potential to support overall wellness. Rich in natural caffeine, Guarana may help promote mental alertness, focus, and healthy energy levels. This remarkable plant has also been associated with supporting endurance and enhancing physical performance.


Catuaba, a potent herb, is appreciated for its potential to contribute to overall well-being. Known for its adaptogenic qualities, Catuaba may help the body cope with stress and maintain balance. This remarkable herb has also been associated with promoting mental alertness, healthy energy levels, and fostering a sense of vitality.

Reishi Mushroom

Reishi Mushroom, a highly-regarded fungus, is esteemed for its potential to enhance overall wellness. With adaptogenic properties, Reishi Mushroom may help the body manage stress and maintain balance. This extraordinary mushroom has also been linked to promoting immune system support, healthy energy levels, and fostering a sense of calm and relaxation.

Astragalus Root

Astragalus Root, a powerful herb, is respected for its potential to contribute to overall well-being. Renowned for its immune-supporting properties, Astragalus Root may help fortify the body’s natural defenses. Additionally, this remarkable root has been associated with promoting healthy energy levels, heart health, and supporting the body’s ability to adapt to stress.

Asian Licorice Root

Asian Licorice Root, a versatile herb, is valued for its potential to support overall wellness. Known for its adaptogenic properties, it may help the body cope with stress and maintain balance. This remarkable root has also been linked to promoting healthy digestion, respiratory function, and supporting the immune system.

American Ginseng

American Ginseng, a revered herb, is prized for its potential to contribute to overall well-being. With adaptogenic properties, it may assist the body in managing stress and maintaining harmony. American Ginseng has also been associated with promoting mental alertness, healthy energy levels, and supporting the immune system.

Rhodiola Rosea

Rhodiola Rosea, a robust herb, is admired for its potential to support overall wellness. As an adaptogen, Rhodiola Rosea may help the body cope with stress and maintain balance. This remarkable herb has been linked to promoting mental clarity, healthy energy levels, and increased endurance.

Peruvian Maca

Peruvian Maca, a nutrient-packed root, is celebrated for its potential to enhance overall well-being. Known for its adaptogenic qualities, Maca may help the body manage stress and maintain balance. This powerful root has also been associated with promoting healthy energy levels, endurance, and supporting hormonal balance.

Schisandra Fruit

Schisandra Fruit, a unique berry, is renowned for its potential to contribute to overall wellness. Boasting adaptogenic properties, it may help the body adapt to stress and maintain equilibrium. Schisandra Fruit has also been linked to promoting healthy energy levels, mental clarity, and supporting the body’s natural defense


Acai, a nutrient-dense berry, is recognized for its potential to enhance overall well-being. Rich in antioxidants, Acai may help support the body’s defenses against environmental stressors, while promoting healthy energy levels and vitality.

Himalayan Goji

Himalayan Goji, a nutrient-rich fruit, is valued for its potential contribution to overall wellness. This superfood is believed to support the immune system, promote healthy energy levels, and aid in maintaining balance within the body. With its antioxidant properties, Himalayan Goji may help protect cells from environmental stressors.

Gotu Kola

The main group of components in gotu kola is the triterpenes including asiaticoside, madecassoside, asiatic acid, and madecassic acid, which have antioxidant and anti-inflammatory properties that are shown to positively influence brain plasticity which means a much sharper you.

  • Exhibits significant wound healing ability, Improves microcirculatory parameters, Sedative and anxiolytic properties, Antidepressant, Re-vitalize the brain and nervous system, increase attention span and concentration and combat aging: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116297/

Water Hyssop

Best known as a neural tonic and memory enhancer this powerful herb increases cerebral blood flow and neurotransmitter modulation.

Green Tea Extract

Healthy energy producer and one of the more researched and promising supplements. It upregulates fat metabolism at rest and during exercise. In recent years the consumption of Green Tea Extract has shown to help prevent lifestyle diseases like cardiovascular disease because of it’s preventative effects on chronic inflammation.

  • Helps with weight loss by increasing a protein hormone which is involved in regulating glucose levels as well
    as fatty acid breakdown:https://pubmed.ncbi.nlm.nih.gov/26093535/
  • Decrease cholesterol absorption and plasma levels, has strong free radical-scavenging
    activity inhibiting LDL oxidation, reduce the adhesion molecule expression, has antitrombotic activities by inhibiting platelet aggregation:https://pubmed.ncbi.nlm.nih.gov/15969262/ 

Mikania Guaco

“Guaco” is Sun Horse Energy founder Dan Moriarty’s favorite herb, and the reason why he’s still alive. Traditionally, it’s a well-known herb for snake bites, scorpion stings and other venomous creatures. Guaco acts as a non-steroidal bronchodilator, meaning it opens up the airways without steroids. As a result of guaco opening up the airways, the alveoli (tiny air sacs in the lungs) are better able to accept oxygen transfer and get rid of carbon dioxide. In Brazil, Guaco syrup is one of the most popular herbal medicines used to treat the symptoms of asthmatic bronchitis, cough and hoarseness.

Osha Root

A traditional Native American herb, Osha is also known as “Bear Root”. Native Americans noticed that when bears emerged from hibernation, the first thing they did after being in a state of torpor for 4 months was not feast on salmon or drink water, but rather, dig up osha and eat it. Why? It decongests and wakes up the lungs. Native Americans who used Osha were able to run further, and treat their colds and congestion. Modern research studies suggest Osha may support the immune system by offering protective effects against oxidative damage.

I want to thank you for your existence. I want you to know that functional medicine has changed my life, well the life of my autistic son. So much so that I plan on taking the Functional Medicine Health Coach Certificate and work with my new friend who is now a Functional Medicine Doctor from the Institute of Functional Medicine and spread the word on GI testing and how finding the underlying issues will help eliminate autistic traits. 

I hope to be able to meet you one day so I can share this great news with others. Changing my son’s diet has changed him. Food is medicine!! By the way, I’m cooking my rutabaga. I’m Italian and never grew up with these. With love.

Rita Mastrangelo

I found you on YouTube a couple of weeks ago and I’m hooked. I listen to you a couple of hours every morning. I am being tested for celiac disease and have been gluten-free for a couple of weeks. Thank you for all of your insight.

April Renee

Just wanted to tell you that you’re amazing! You are helping so many people all over the world! Including me! Thank you so very much, Dr. Tom O’Bryan!

Patricia Puddle

Good morning Dr. Tom, Would just like to say thank you! This time last year I was going through a hell of a time with my gut. Terrible indigestion on a regular basis, feeling as if I had eaten a boulder and the tiredness was doing my heed (scottish for head) in! With two young girls being tired is not an option!

I went to the doctors on a number of occasions and they decided to prescribe omeprazole to mask the problem, sorry help my problem. I decided taking these drugs was not an option for me! So I started googling the life out of it!! Low and behold you started popping up!! Oh and Gluten intolerance! 

Your advice has been second to none! You have in my case really simplified what gluten does to my body and now that I have cut it out (which as it appears in lots of foods, some I can’t understand) I have found that my symptoms very quickly reduced and now I’m a year down the line they have gone for the vast majority of the time!! For that I’m truly grateful. I now follow you on YouTube and Instagram, which continues to educate me and the importance of gut health. I look forward to your future advice. Yours faithfully,

Gary Christie

Black Ant Extract

A Chinese medicine tonic, Black Ant is used to support energy levels. (In traditional Chinese medicine, Black Ant is given to increase vital Qi.) Research studies demonstrate that Black Ant supports the function of the thymus gland, which plays a crucial role in the immune system, producing and activating lymphocytes.

Siberian Ginseng

This well known adaptogen has been proven to reduce cardiovascular stress, lower and stabilize blood sugar to healthy levels, and encourages a more efficient lipid metabolism.

Pine Bark Extract

Many studies have shown that pine bark possesses anti-aging properties. It’s very similar in nature to the well-known antioxidant and anti-inflammatory compound, resveratrol, which is abundant in red wine and grapes. Pine bark has a proven beneficial effect on lipids, the cardiovascular and immune systems.

Lion's Mane

A very yummy and medicinal mushroom is a well established candidate for brain and nerve health because it triggers neurite outgrowth and regenerates damaged nerves. Lions Mane has been extensively studied for its neuro-health properties.


This is an enzyme/protein that speeds up biochemical reactions and helps to prevent and dissolve the formations of blood clots (thrombi); addresses the problem of blood hyperviscosity, thereby preventing thick and sticky blood, which is not conducive to overall cardiovascular health.


Referred to as the women’s ultimate power herb, by some herbal enthusiasts. Used in India for at least 3,000 years, Shatavari, is structurally similar to estrogen produced within the body. Some researchers have concluded shatavari can be a highly effective alternative to synthetic hormone replacement therapy for peri- and menopausal women.

Chaste Tree Berry

Improve female libido, mitigate PMS, reproductive health

Horny Goat Weed

Increase para-sympathetic nervous activity, mitigate osteoporosis, improve libido, enhance smooth muscle tissue function

  • Treatment for erectile problems and nerve injuries in human patients:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551978/
  • Prevents thickening or hardening of the arteries through multiple mechanisms, including attenuating DNA damage, correcting endothelial dysfunction, inhibiting the proliferation and migration of smooth muscle cells, repressing macrophage-derived foam cell formation and inflammatory responses, as well as preventing platelet activation:https://pubmed.ncbi.nlm.nih.gov/29075193/

Bulgarian Tribulus

Enhance athletic performance, improve circulation, improve sexual performance, more efficient rates of protein synthesis


Cordyceps, a genus of mushroom, gained lots of attention after Chinese long-distance runners performed impressively at international competitions in the 1990s and early 2000s. Along with high-altitude training, supplementing with cordyceps was part of their intense training program. A research study concludes that cordyceps improves tolerance to high-intensity exercise after supplementation with it because the fungus is thought to increase blood flow, enhance oxygen utilization; it also acts as an antioxidant. It also has powerful anti-tumor properties, the ability to regulate the endocrine system, enhance your immune function, and protect the kidneys, lung, liver, and other organs.

  • Immunomodulatory, antitumor, anti-inflammatory, and antioxidant activities, promotion of endurance capacity, and learning-memory improvement, can be used to treat conditions such as hyposexuality, night sweats, hyperglycemia, hyperlipidemia, asthenia, arrhythmias, and other heart, respiratory, renal and liver diseases: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924981/
  • Various pharmacological actions, including nephroprotective, hepatoprotective, anti-inflammatory, antioxidative, and antiapoptotic effects:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849494/

Ginkgo Biloba

In recent decades, an extract of the leaves of the tree Ginkgo biloba L. has been used to improve memory in disorders like Dementia disorders that affect memory and intellectual functioning, and are caused primarily by Alzheimer’s disease and vascular disorders.

  • Potent antioxidant properties and ability to enhance peripheral and cerebral circulation, ginkgo’s primary application lies in the treatment of cerebrovascular dysfunctions and peripheral vascular disorders:https://pubmed.ncbi.nlm.nih.gov/11565403/
  • Experimental results showed extracts of G.Biloba to upregulate protein expressions of BDNF:
  • The effects of Ginkgo biloba extract on cognitive functions in aged female rats;
  • The role of oxidative stress and brain-derived neurotrophic factor: https://www.ncbi.nlm.nih.gov/pubmed/25446810


Jiaogulan, a versatile herb, is celebrated for its potential to support overall well-being. Known for its adaptogenic properties, Jiaogulan may help the body cope with stress and maintain balance. This remarkable herb has also been associated with promoting healthy energy levels, boosting endurance, and fostering a sense of calm and relaxation.