Understanding the True Cause of Autoimmune Disease

This article was originally published by our friend Dr. Amy Myers 

My mission as a functional medicine doctor and a New York Times Bestselling author 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 I want to help you get to the root of your autoimmunity so that you can take your health back in your own hands and avoid the harsh treatments that I was forced into by conventional medicine.

There is a 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 like I was, 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.

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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. Infection

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.


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Amy Myers, MD is a renowned leader in Functional Medicine and New York Times Bestselling author of The Autoimmune Solution. She received her Doctorate in Medicine from LSU Health Sciences Center and spent 5 years working in emergency medicine before training with the Institute of Functional Medicine. She has helped thousands around the world recover from chronic illness through her dietary based program, The Myers Way, and she has created multiple interactive eBooks and eCourses to guide readers through her revolutionary approach to health. Her blog and website serve as a beacon of hope to the many sufferers of chronic disease and autoimmune conditions. Her book: The Autoimmune Solution, a 30 day program to prevent and reverse the full spectrum of inflammatory symptoms and disease, is now available at all book retailers.