Understanding the True Cause of Autoimmune Disease

March 4th, 2016

Understanding the True Cause of Autoimmune Disease

March is Autoimmune Disease Awareness Month! In honor of that, I want to highlight some of my most helpful articles about autoimmune disease over the next four weeks. My mission is to empower others by providing them the tools I wish I had when conventional medicine failed me during my own struggle with autoimmune disease. That’s why these articles are packed with important information and practical tips to help you get to the root of your health problems and reverse your condition.

Follow along as we explore how to optimize your diet, heal your gut, and make lasting lifestyle changes to calm your inflammation and eliminate your symptoms. Plus, I’ll be offering special sales on the supplements and resources that are most helpful for those with an autoimmune disease. Be sure to sign up for my free weekly newsletter so you don’t miss out!

The first topic I want to tackle this month are the true causes of autoimmune disease, and the huge disconnect between what actually causes autoimmunity and how conventional medicine treats it. If you are frustrated by the conventional medicine approach to your health and well-being, I hope this information will help you discover that there is another way to treat autoimmune disease, and you can reverse your condition!


Autoimmune Disease: A Disease Of The Immune System

The first thing to understand about autoimmune diseases is that they are a disease of the immune system. If you have an autoimmune disease, somewhere along the way your immune system went rogue and began attacking your own tissues. In some cases it’s your thyroid under attack, in others it’s your intestines, your skin, your brain, your pancreas, or another organ. But no matter what part of your body is under siege, the culprit is your immune system. This means that in order to treat, prevent, and reverse autoimmune disease you’ll need to get your immune system back under control.

However, under our current medical system, autoimmune diseases are not recognized as diseases of the immune system as a whole. Instead they are treated as diseases of particular organs. Unfortunately, that means that there isn’t a unified branch in conventional medicine to treat autoimmune conditions. With cancer for example, we have cancer specialists called oncologists who treat many different types of cancers no matter which organ system they involve. Yes, there are some sub-specialties within oncology, but they typically still fall under one main oncology umbrella.

If, on the other hand, you are suffering from an autoimmune disease, you will see a specialist who focuses on the organ system that is being affected: a rheumatologist for rheumatoid arthritis; an endocrinologist for Hashimoto’s and diabetes, a gastroenterologist for celiac, ulcerative colitis and Crohn’s; a dermatologist for psoriasis; and so on. If you have multiple autoimmune conditions, as many people do, you will see several different specialists, each of whom will likely prescribe a different medication. And, there is a good chance that none of these specialists will look at how to strengthen and support your immune system, which leads me to my next point.


Supporting, Rather Than Suppressing, The Immune System

In conventional medicine, the belief is that once you have an autoimmune condition, there’s nothing you can do to reverse it, only ways to manage the symptoms. Managing the symptoms typically involves harsh medications that are aimed at suppressing your immune system. While these medications can be effective at reducing some of the symptoms of the disease, since they suppress the entire immune system, they are not without many unwanted side effects such as fatigue, weight gain, depression, increased infection rates and even cancer.

In contrast, functional medicine sees the body as a whole and works on the principle that the health of one system impacts the health and function of the others. Instead of focusing on disease symptom management, we focus on supporting and strengthening the immune system by getting to the root of why the immune system went rogue in the first place. While there is no known cure for autoimmune disease, I believe that there are five key elements that are at the root of all autoimmune conditions. In my functional medicine practice I have been able to successfully help hundreds of patients lower and reverse antibodies, get off their harsh medications, and become symptom free.


5 Underlying Causes of Autoimmune Disease

1. Leaky Gut
The gut is the gateway to health, it houses 80% of your immune system, and you can’t have a healthy immune system without a healthy gut. Thanks to research from Alessio Fassano (and I’ve confirmed it in my own practice), we now know that if you have an autoimmune disease your gut has become leaky, meaning the tight junctions that typically hold your gut lining together have become loose, allowing undigested food particles, microbes, toxins, and more to escape your gut and enter your bloodstream.

All of these particles are recognized by your immune system as foreign invaders, sending your immune system into high alert and triggering a huge rise in inflammation. This continual strain on your immune system eventually causes it to go haywire, and it ends up attacking your own tissues by mistake.
2. Gluten
Gluten contributes to autoimmune disease in three key ways. First, it is the primary cause of leaky gut because gluten triggers the release of zonulin in your intestines, a chemical that tells your gut lining to “open up”. Second, it is highly inflammatory, meaning it stresses your immune system. Thirdly, the gluten protein has a similar chemical structure to some of your body’s tissues (specifically your thyroid), which can lead to molecular mimicry, where your body mistakes your tissues for gluten and attacks them. You can read more about how gluten impacts autoimmunity in this article.
3. Toxins
Toxic molds (mycotoxins) and heavy metals such as mercury are the two main toxins I see in those with autoimmune conditions. Mycotoxins are very volatile compounds produced by toxic molds that wreak havoc on the immune system.

We are exposed to heavy metals like mercury in different ways: mercury amalgam fillings in teeth, fish consumption, and the environment. Mercury is toxic to our bodies and can be one piece of the puzzle for those with autoimmune diseases.
4. Infections
Scientists have long suspected that infections from bacteria, viruses, and other toxins were likely to blame for the development of autoimmunity. There are now a number of infections, including Epstein Barr (the virus that causes mono), Herpes Simplex 1 and 2, E. coli, that have been linked to autoimmune diseases
5. Stress

Levels of stress-related illnesses are on the rise, and stress, both of the emotional and the physical variety, has been shown to trigger and intensify autoimmune disorders. Stress disrupts immune function through several distinct pathways.  Stress is the body’s response to a threat–a wound, injury, or infection. Chronic stress (the kind we face in this day and age) leads to long term inflammation that never really shuts off, creating autoimmune disease. Once the autoimmune response is in place, immediate stress only exacerbates it.


The Myers Way® Approach to Reversing Autoimmune Disease

1. Heal your gut.
Healing your gut is essential to healing yourself. After all, 80% of your immune system lies in your gut! For this reason, I created The Myers Way® Guide to the Gut eCourse to help guide you through the exact same steps I use with my patients to heal their guts. I also have many articles explaining my 4R approach  to healing the gut and gut-healing supplements.
2. Remove gluten, grain, and legumes from your diet.
For my patients with autoimmune diseases, I highly recommend removing not only gluten but all grains and legumes from their diet. These foods contain proteins known as lectins, which act as a natural pesticide for crops and can wreak havoc on the lining of your gut. Changing your diet is the first step in getting well. I created The Myers Way® Comprehensive Elimination Diet eCourse which you can do at home, and it’s the foundation that I use with my patients to begin recovering from illnesses. There is a special autoimmune protocol in the eCourse.
3. Test for heavy metals and mycotoxins.

I recommend having your MTHFR genes tested and doing a DMPS chelation challenge test through a functional medicine practitioner to determine if mercury or other heavy metals are an issue for you. Real Time Lab has the test I use for assessing if someone is being exposed to mycotoxins. I also recommend that all my patients find a biological dentist to remove their mercury amalgam fillings.

4. Find and treat infections.
There are a number of bacterial and viral infections that have been associated with autoimmune conditions. Have your doctor test for infections such as HSV and EBV.  Monolaurin from coconut oil can be very effective treatment for both HSV and EBV.  Lysine and a lysine-rich diet is effective at treating HSV infections.
5. Manage your stress.
I tell all my patients that they should prioritize stress reduction. Take care of yourself by adopting some stress-relieving strategies, such as exercise, meditation and art. If you are having trouble relaxing, try a yoga class or a guided meditation. I use a heart rhythm pacer called InnerBalance, an app that coaches you to breathe in line with your heartbeat.  Even giving yourself five minutes to sit quietly with a fragrant cup of herbal tea (caffeine-free, of course!) can help tremendously.

My approach is based on getting to the root of the problem: removing the elements that derailed your immune system in the first place and strengthening your immune system rather than suppressing it. That’s why using this approach enables you to reverse and prevent many different autoimmune conditions at once.

Want to learn more about preventing and reversing autoimmune disease?



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  • Julia Reagan

    I have been saying for years my MD’s need to get to the cause instead of the controlling the symptoms. Every time I would visit my MD, I would test positive for some auto immune disorder (my interpretation), not hers. I have been telling her for years that food affects the many debilitating symptoms of all of my issues.

    So glad to have found someone that really understands my views and is so knowledgeable about how to treat and alleviate some of these symptoms.

    I had to retire early due to pain, inflammation, fatigue, depression,(you know, all of the symptoms), but trying to survive on my disability and meager retirement is not cutting it. I refuse to accept that this is my life from here on out. Please keep the great articles coming!

  • Angela

    Dr. Myers, Could you please comment on Scleroderma in regards to your findings, there is so llittle information out there and before I start your program I would appreciate your insight!

  • Christi Clapp Beechwood

    This is so interesting! Thanks for all the good info. Have you heard of Korean spa treatments curing issues related to autoimmune diseases? I have Celiac disease and get bumps on my hands and feet when I’ve been ‘contaminated’ with gluten. Since going to a Korean spa and doing all of the various saunas, I have had NO bumps (and few GI issues), even though I’m positive I’ve been contaminated. I was thinking maybe it healed some of the leaky guttiness…but just wanted to know if it’s something you’ve heard of before. Love what you’re doing, and that you’re changing modern medicine! Thanks again!

  • Dawn

    Dr. Myers thanks for such a great information. I would like to echo Angela’s request below for your insights on Scleroderma. Thanks!

    • Because autoimmune diseases are diseases of the immune system and not of the organs which they affect, I treat them all similarly. Of course I tailor to specific circumstances, but my approach to autoimmune scleroderma is going to be relatively the same!

  • Dori

    Dr. Myers I just now learned of your site and would like to know your thoughts on an autoimmune illness that I have been suffering with since 1997. The name of the autoimmune illness is Dermatomyositis. I would very much appreciate any insight you may be able to give me. Thank you.

    • Hi Dori–Dermatomyositis is an autoimmune disease and therefore I view it as a disease of the immune system, not of the skin and the muscles. I’m hosting a free summit next month all about autoimmunity–you should tune in!! it’s completely online and packed with tons of information from 40 experts in autoimmune disease. You can register here: http://www.autoimmunesummit.com

  • jm

    For the last year I have been having IVIG treatment for Chronic Inflammatory Demyelinating Polyneuropathy. When starting treatment this seemed like the only option to control the condition and that I had no hope of reversing it. In order to try the approaches you suggest do you need to stop all conventional treatments to be in with a chance of reducing/ reversing your condition or can you do both? Many thanks.

    • Many of these things can be done while you’re going through conventional treatment, but always check with your primary care doctor or see a functional medicine doctor like me before you change or reduce your medication!

  • vickiogrady

    Dr. Myers, I am a 47 year old menopausal woman who has always been the picture of health up until two months ago. In July I started seeing a nathopathic dr and begun taking fistfuls of supplements. From UTI care to Addrenal support. I have also been on 137 mcg of Synthroid for many years. After about six weeks on these supplements I developed Oral Lichen Planus and burning mouth. I immediately stopped the supplements. It has been almost two months and my mouth is getting worse. I have seen seven Dr’s total from my MD to Oral surgeons. Only one Dr said it was Lichen Planus all the others didn’t think it was. I feel like the supplements upset the balance in my body…..HELP! This is ruining my life! Sincerely, Vicki

    • AJfromLA

      I had burning mouth for years and was told by many doctors that it was autoimmune and there was nothing that could be done. I finally mentioned the complaint to my Osteopath and she took one look at my tongue and proclaimed it was food sensitivities. We did a comprehensive test and I was sensitive to a LOT of foods and substances. I took those out of my diet and no more burning mouth.

    • Vicki I’m so sorry to hear that you’re going through that! I would love to see you as a patient at my clinic: http://www.amymyersmd.com/become-a-patient/

  • Kayla Schriber Yates

    I am a mother of 3 daughters, my youngest (will be 2 this
    month) has had quite a journey this last year. When she was 6 months old, I
    took her for her wellness checkup and questioned the doctor about some blood in
    her stools. Was told it was anal fissures, caused from straining and that she
    would grow out of them. I wasn’t convinced because she had loose stools. At the
    9 month checkup, I questioned him again and now she had nose bleeds along with
    the blood in the stools. He again told me fissures and probably sinus or
    allergies. Due to my persistence and concern, he gave us an antibiotic and sent
    us to a pediatric GI doctor that came to the same conclusion. When she was a
    year old, she still had blood in the stools, chronic nose bleeds and now a
    mouth ulcer. They did labs which showed elevated blood counts. They sent us to
    a hematologist to check for bleeding disorders (none found). In April of this
    year, she became severely sick and spent 14 days (4 in PICU with 105 fever) in
    the hospital. The bleeding became worse, and the ulcers spread throughout her
    entire mouth and so severe she could barely take fluids. They did numerous
    tests and procedures. One was IVIG transfusion and an upper/lower scope with a
    biopsy of the colon. The scope showed 3 lesions but not much more. They have
    tested her for HIV, cancer, Kawasaki, Cat Scratch Fever and several other
    things. Basically if there was a test/procedure they did it. They discharged
    her with an atypical form of Behcets. This last month we had a scope performed
    on her nose with a biopsy. Both biopsy were inconclusive. We have now seen 2
    hematologist, 2 GI doctors, 2 cardiologist, a nephrologist, ENT and 2 rheumatologist.
    All of them give us the same answer: “Your
    daughter is unique and we have never seen a case like hers.” We have been
    gluten free, dairy free and soy free since April. We also give her probiotics,
    digestive enzymes, multivitamin with extra zinc, vitamin D drops, and now iron
    once a day. She is also taking a blood pressure med (2x daily), immune suppressant
    and a steroid daily. The blood in stools is better and no more mouth ulcers,
    but chronic nose bleeds are worse. We are getting ready to go to an
    immunologist, but not expecting much. We are getting very frustrated and just
    not sure where to turn next. Any suggestions?

    • Laura Haskett Cole

      I would recommend going to a pediatric specialist at Children’s Hospital in Cincinnati. They saved my son’s life when he was a baby (he had a zinc deficiency related to prematurity, and you would not believe how many doctors misdiagnosed him). I would recommend an endocrinologist or GI doctor.
      Best of luck to you and your family.

    • Hi Kayla, I’m so sorry you’ve had to go through all of this. I completely understand how frustrating it is. Have you looked at the Institute for Functional Medicine? They have a great search tool on their site to find functional medicine doctors like me: https://www.functionalmedicine.org/practitioner_search.aspx?id=117

  • Joanna

    Hi Dr. Myers, our family has been exposed to a lot of mold in the home. How would one detoxify from it?

  • YIBF

    Dr. Myers would you consider Systemic Mast Cell disease an autoimmune disease?

  • Evelyne Tilsner

    I wonder if this advice helps if you suffer from Morbus Addison? Any idea please?

  • Stephanie Medina

    There was a doctor in the autoimmune summit who was conducting a thorough study and testing foods to see the effects of antibodies and determined if there was truly an effect. I recall him saying legumes did not produce a reaction as most had once thought. Can you clarify if I am remembering this correctly and what was the doctors name who is conducting this research? I might have seen it on another interview but i don’t really remember. Thank you!

  • marie carr

    Hmm…Interested in the last paragraph of this article …

    ”My approach is based on getting to the root of the problem: removing the
    elements that derailed your immune system in the first place and
    strengthening your immune system rather than suppressing it. That’s why
    using this approach enables you to reverse and prevent many different
    autoimmune conditions at once.”

    I was diagnosed with rhuematiod arthritis 4 years ago after I must admit a VERY stressful birth with my 2nd child and I have been on Methotrexate and hydroxycloroquine ever since and now am able to walk without a walking stick and am more or less pain free except for the odd times – you talk about strengthening the immune system but my rhematologist tells me that my immune system is the very thing attacking me! why on earth would I want to strengthen that?! My immune system is being suppressed so that my joints don’t swell and cause me discomfort and pain!

    • In autoimmune disease, the immune system is misguided. Suppressing it doesn’t get to the root of the problem–it just puts a bandaid over the symptoms (a dangerous thing to do, since a strong immune system is necessary to fight off infections). In my experience, once we can get to the root of the problem, we can shut off the misdirected immune response and get it back to a normal, strong and healthy immune system!

  • Nadine Stilon de Piro

    I suffered the symptoms of fibromyalgia for many years and was diagnosed about a year ago. I did all the above, and each one helped a bit but what I finally discovered was that I have had a long standing allergy to nickel which has been there for some forty years, I just didn’t know it was in food. the chronic attacks were probably aggravated when my immune system dropped due to stress. I believe it was the long standing inflammation in my body triggered the autoimmune dysfunction..Since i began my treatments my symptoms have fallen away. of course i still have to watch the nickel but feeling much much better.

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  • lucy1535

    well, what about scleroderma

    • Hi Lucy, I generally use the same approach for any autoimmune disease.

  • Kim

    Dr. Amy, 4 year old began losing hair on the top of his head and the dermatologist said it is alopecis, an auto immune disease. I never heard of auto immune diseases and found your article above helpful and will order your book. Have you found these 5 steps help with alopecia in any of your patients? Thanks Kim

    • I treat alopecia the same way I treat any autoimmune disease, although I have not always seen as much success with it

  • Amy Williams

    Hi Dr. Meyers. I have been diagnosed with both Crohn’s disease and Ankylosing Spondylitis and Congenital Emphysema (i have never smoked or lived near a smoker, yet I have lung destruction)….all of which are auto immune (even the Emphysema is suspected to be auto immune related since they cannot find any other cause). My symptoms really started appearing in 2012. A short time before this, I had all of my mercury fillings removed (I had read about how dangerous they can be), but unfortunately I did not know that they needed to be removed in a particular safe manner. The Dentist just drilled them out. I am wondering if this could have been a trigger for my auto immune diseases? How do I test my mercury levels? I don’t seem to have the typical symptoms described Online for mercury poison. By the way, I have been off all grains and starches since 2012, thanks to Dr. Ebringer in London, who feels that Ankylosing Spondylitis is caused by an infection from Klebsiella. His website is: http://www.KickAS.org . The diet helps me tremendously. But I still have 1 major flare up per year, which results in hospitalization. When my AS flares up, my Crohn’s also flares and visa versa. Doctors want me to take Humira but I refused. I would rather have 1 flare up per year that suppress my immune system every day of the year.

  • Amy

    Dr. Myers, my doctor wants to chelate me for an elevated level of arsenic. My mercury was fine on a provoked test with EDTA. If my mercury was fine is there any reason to get rid of my amalgam fillings? Can EDTA pull out more mercury into my system?

    • Though I can’t advise you without seeing you as a patient, I will say that studies have shown that amalgam fillings continue to emit mercury vapor for a long time. I generally recommend that my patients have them removed.

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