Written by Elizabeth Boham, MD
A New Approach to Autoimmune Disease

A New Approach to Autoimmune Disease

“Autoimmune disease” might just sound like a strange combination of words, but every day it becomes more and more relevant to our health. Fifty million Americans have one or more autoimmune diseases, and that number is rising. An autoimmune disease occurs when the body mistakenly attacks its own tissues, and this can lead to a wide range of symptoms throughout the body.¹ There are many different autoimmune diseases, including autoimmune thyroiditis, multiple sclerosis, rheumatoid arthritis, Crohn’s disease, and lupus. The rise in autoimmune disease parallels an increase in allergies and cancer and a decrease in infectious diseases, creating the basis for the hygiene hypothesis.² This theory suggests that as society becomes more obsessed with cleanliness to avoid becoming sick, many people’s bodies are losing their ability to distinguish between self and non-self, causing the immune system to make more mistakes.³ 

At the recent annual conference for the Institute for Functional Medicine in Hollywood, Florida, experts in autoimmune disease from all over the world gathered to take a different look at this problem and discuss solutions. In conventional medicine, I was taught that the most important step in my medical workup of the patient was the diagnosis. When I named the disease, I could then come up with a therapy (often medication) to suppress the disease. Functional medicine thinks about this process differently. Ten people with autoimmune thyroiditis may have ten different reasons that it occurred. Functional medicine doctors focus on recognizing the underlying cause for a condition and work on remedying it. Often, this is much more effective than a quick medicinal fix for the symptoms of a problem. 

Focusing on why someone has an autoimmune disease is very important. If I can identify a person’s imbalances or risks for autoimmunity, I can better help his or her body regain balance and heal. All of the speakers at the conference agreed on the fact that a person often has multiple factors coming together to cause autoimmunity. This could be genetic predisposition, changes in gut permeability, or environmental triggers such as a poor diet, changes in the microbiota in the body, antibiotics, illness or infection, or toxins. In Functional Medicine, the first step is to acquire a detailed patient history in order to find clues as to why the patient developed an autoimmune disease. This gives us better tools for addressing their problem on the deepest possible level.

There may be signs of autoimmunity years before the disease actually develops. If auto-antibodies are present without any other symptoms that signal disease, it can be possible to prevent its progression through beneficial lifestyle changes.

So, what can you do? Here are my recommendations to keep your immune system strong and avoid the triggers that can lead to autoimmunity: 

1.  Mind Your Microbiome – The word “microbiota” is used to describe the trillions of bacteria and yeast that line all areas of each person’s body, from our intestines, to our skin, and even to the inside of our nose.⁴ These good bacteria have a large influence on our immune system and our immune tolerance. Studies have shown that changes in our microbiota (dysbiosis) have been linked to many autoimmune diseases.⁵ Although there is still much that we have to learn about the microbiome, there are a few things we can all do to take care of our microbiota. Avoid unnecessary antibiotics, eat a diet rich in fiber to feed good bacteria, choose meats raised without antibiotics, and consider taking a probiotic. You can find a list of our favorite probiotics on our online store right here.

2. Consume Omega-3 Fatty Acids – Omega-3 fats are bursting with anti-inflammatory properties. Studies have shown that a diet rich in omega-3s decreases the risk of many diseases, including autoimmune disorders like rheumatoid arthritis.⁶ Try to eat fatty fish, like wild-caught salmon or sardines, twice a week. Many people also benefit from taking fish oil capsules. Get your fish oil from a company that uses third-party testing for toxins. A few good brands include Nordic Naturals, Udo’s, and Carlsons. 

3.  Get Tested for Celiac – Celiac disease is an autoimmune condition that occurs in genetically susceptible individuals when they consume any foods that contain gluten, a type of protein found in wheat, rye, and barley. When someone has an autoimmune disease, they are at a greater risk of developing other autoimmune diseases as well. So, if you’re dealing with any type of autoimmunity, it is a good idea to get your blood tested for celiac disease.⁷ If needed, a gastroenterologist will do a biopsy of your intestine to look for the changes that often occur in the villi when a person develops celiac. It is important to remember that people with celiac disease can have a variety of symptoms. Some people have gastrointestinal symptoms, like diarrhea, bloating, and belly pain, while others have fatigue, anemia, osteoporosis, problems with coordination, headaches, and even changes in skin and hair. Additionally, while some people test negative for celiac disease, they may still feel better on a gluten-free diet, either because they are in the early stages of celiac disease or they have a gluten intolerance. If someone has celiac disease, they need to avoid gluten completely and permanently so that their gut and the rest of their body can heal. Many times, a gluten-free diet can help other autoimmune diseases go away as well. 

4.  Intestinal Permeability – The intestinal barrier is the boundary between the inside of the intestines, where food passes through, and the inside of the body. It is very important for that barrier to work sufficiently so that the immune system can function properly as well. When there is a breakdown in the intestinal barrier, which is often known as increased intestinal permeability or leaky gut, immune dysfunction can occur.⁸ Creating a well-working intestinal barrier is extremely important for overall health and wellbeing. The first 1,000 days of an infant’s life are critical for establishing this important barrier to outside invaders. Vaginal delivery, breast feeding, and proper nutrition all help establish the appropriate milieu in the intestines.⁹  As I mentioned above, probiotics also play an important role in maintaining optimal gut health. 

5.  Stress Matters –  A very important aspect in maintaining health and immune system function is to avoid stress. It is easier to catch a circulating cold when we are under stress, and autoimmune disease works in the same way.¹⁰ As the general number of adverse childhood experiences increases, so does the risk for negative autoimmune health outcomes, such as worsening disease and hospitalization because of the disease. The most important part of stress, however, is how we react to it. Our body works better when we perceive a sense of control over our stress. This is why stress reduction techniques, such as yoga, meditation, keeping a gratitude journal, and exercise, really matter. These practices can help decrease the severity of existing diseases and reduce your risk of developing an autoimmune disease.

If you have a family history of autoimmune disease, have elevated autoantibodies without signs of disease, or have been diagnosed with autoimmune disease, there is a lot you can do to improve your health. Delve into what may be out of balance in your body and work to get it back on track. I highly recommend finding a Functional Medicine doctor in your area so that you have comprehensive support throughout this process. Use these helpful tips to find the optimal health you’ve been looking for, and soon your life will be back in balance.


  1. American Autoimmune Related Diseases Association, Inc. https://www.aarda.org/news-information/statistics/#1488234345468-3bf2d325-1052
  2. The World Incidence and Prevalence of Autoimmune Diseases is Increasing https://pubs.sciepub.com/ijcd/3/4/8/
  3. Eat Dirt — The Hygiene Hypothesis and Allergic Diseases https://www.nejm.org/doi/full/10.1056/NEJMe020092
  4. Microbiota at the crossroads of autoimmunity https://www.sciencedirect.com/science/article/pii/S1568997216301471
  5. The human microbiome in rheumatic autoimmune diseases: A comprehensive review  https://www.sciencedirect.com/science/article/pii/S1521661616302480
  6. Relationship Between Fish Consumption and Disease Activity in Rheumatoid Arthritis. https://www.ncbi.nlm.nih.gov/pubmed/28635117
  7. Celiac Disease and Autoimmune-Associated Conditions https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741914/
  8. Zonulin, regulation of tight junctions, and autoimmune diseases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384703/
  9. The microbiome in early life: implications for health outcomes https://www.nature.com/articles/nm.4142
  10. Cumulative Childhood Stress and Autoimmune Diseases in Adults https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318917/

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