The Functional Medicine Approach to Autoimmunity

The Functional Medicine Approach to Autoimmunity

Dr. Jennifer Kessmann MD IFMCP Dr. Jennifer Kessmann, MD
Functional Medicine Doctor
Autoimmune Diseases Expert

What is it | Causes | Diet | Balance an overactive immune system
Autoimmune diseases are among the most prevalent diseases in the U.S with more than 23.5 million Americans affected.[1]
Is there anything we can do to treat or prevent these serious and debilitating illnesses in a more natural way?

While genetics plays a role in the development of autoimmune disease, we now know that lifestyle and environmental factors can trigger an immune response that may lead to autoimmunity. And many of these factors, such as your diet, are in your control.

In this article, Dr. Kessmann helps us understand some of the key steps you can take that can help you manage your autoimmune symptoms to improve quality of life. The information in this article is meant to educate you about the various lifestyle options for autoimmunity and help you discuss the best treatment plan with your doctor.

Related post: Autoimmune diet.

What is an Autoimmune Disease?

Autoimmunity happens when our immune system gets confused, overreacts and starts to attack the body’s healthy tissues. This immune over stimulation causes a broad range of illnesses, known collectively as autoimmune diseases. The damage is generally targeted to one body system or organ. For example, when the immune system attacks the islet cells of the pancreas, type 1 diabetes results. When it attacks the joints, this leads to rheumatoid arthritis.

“A splinter that never goes away”

The same immune activation process designed to protect us from an infection or an injury can also lead to autoimmunity, if it gets off track. This immune dysfunction can be propagated by genetics, environmental exposures or other situational factors that play a role in immune system regulation.

When you get a splinter, for example, you may notice redness and swelling. Immune cells are sent to the site to help push the splinter out and treat any infection. Healing then occurs and scar tissue is formed. This process is all effectively managed by our immune system.

But, what if the splinter never goes away? In this case, the immune system continues to amplify the response. At some point, the response becomes excessive, and may lead to autoimmunity through the damage to the nearby tissues.

When the immune system gets out of control

When the immune system gets out of control

“I like to think of our immune system as an orchestra.” explains Dr. Kessmann. As long as the sections play in harmony with each other the orchestra is beautiful. If one section is playing out of control the orchestra is out of balance.

This is similar to what happens with the sections of our immune system. It is important for it to be balanced, different parts turning on and turning off quickly so that unintended damage does not occur to our own tissue. Prolonged responses to unintended substances is termed “loss of tolerance”. When this occurs the immune system is overreacting full steam ahead amplifying certain parts creating potential damage in its path leading to disease. The damage to our own tissues further promotes unintended immune responses and further amplifies the problem.

What Causes Autoimmune Disease?

Genetics vs. epigenetics

potential causes and risk factors that may contribute to autoimmunity


While genetics does play a role in autoimmunity, certain lifestyle and environmental factors can “turn on and off” specific genes that can trigger the immune response. This is referred to as epigenetics.

Very often there isn’t one distinct cause, but rather a combination of factors that can contribute to and lead to autoimmune issues.

Common potential causes that may contribute to autoimmunity include:

  • Ongoing Infections: such as viruses, parasites, bacteria, Lyme disease, and oral infections.
  • Environmental stimulus and toxins: such as pesticides, herbicides, GMOs, heavy metals, and mold exposure.
  • Food allergies and sensitivities
  • Physical trauma/injury or damage to tissue
  • Psychological stress: Activates the sympathetic fight or flight nervous system. This mechanism is designed to help us survive in life threatening situations. When triggered too long, however, it can increase the risk of autoimmunity.
  • Electromagnetic fields (EMFs): A growing body of evidence links electromagnetic fields sensitivity to immune system activation and autoimmunity. While we still need to learn more to fully understand EMFs full effect, I believe it is very beneficial to limit your EMFs exposure if you have an autoimmune disease.
    To learn more, read my article on EMFs & Your Health.

Your Diet & Autoimmunity

Your Diet & Autoimmunity

Food can influence immune system activity. Removing reactive foods can help to calm the immune system activity and promote health. This is through an elimination type diet. It is also important to rotate the remaining foods that you are eating to prevent an unintended response if you have leaky gut or immune system upregulation. We usually recommend a four day cycle in between each exposure. This can help to prevent reactions to new and healthy desirable foods.

Autoimmunity & Molecular Mimicry

One possible explanation of how food triggers autoimmunity is known as molecular mimicry. Molecular mimicry means that protein structures of some foods are quite similar to the structure of certain organs in the body. If you eat these foods when your gut is damaged, for example when you have intestinal permeability or a leaky gut, it may allow whole, undigested proteins to enter the bloodstream. When the immune system spots these whole proteins from food, it starts to mount an immune response against them as a way to protect you from perceived danger. Food is best broken down by enzymes and digestive acids in the stomach and small intestine. Activation of the vagal system helps to digest our food and prevent autoimmunity in that way.

Because the protein structures of some foods are similar to the structure of certain organs, the immune system may not always distinguish between the body’s own tissue to the food, and mistakenly attack the “matching” organ. The immune system has now mounted an attack against the body’s own organ, seeing it as the enemy.

Dairy for example, has a molecular mimicry to cartilage, which can play a role in rheumatoid arthritis. Gluten, another food known to trigger immune reaction, has molecular mimicry to thyroid and cerebral tissue, which may be linked to Hashimoto’s disease and Cerebellar ataxia.

Avoiding or eating these foods will not prevent or cause autoimmune disease if other factors, like genetics, are not also involved. But, if you are struggling with autoimmunity or have a genetic predisposition, your diet can make a big difference. We’ll cover the autoimmune diet in much more details in the next sections below.

Creating a Balanced Immune System

Creating a Balanced Immune System Autoimmunity

When you have autoimmunity, the overactivated immune system becomes so sensitive, it can react to things that would normally not cause any issues. To address that, it is very important to limit known triggers, and calm the immune system.

While the treatment varies from one person to another depending on their individual situation, some of the key components include:

Address underlying infections

Microbial imbalances, Lyme disease, as well as dental, sinus, and bladder infections can trigger the immune system. If you have an underlying infection, it is critical to work with your doctor to get it treated.

Heavy Metal Exposure

Heavy metal toxicity from dental amalgam fillings, contaminated fish and other environmental sources can cause ongoing immune system reactivity leading to autoimmunity. If this is a concern for you, work with a qualified health care professional and check your heavy metal status.

Activate T-regulatory cells

Back to the immune system – orchestra analogy. Just like the conductor needs to control the all the sections of the orchestra to maintain harmony, T-regulatory cells are able to calm an over reactive immune system. With autoimmunity, they often become deactivated, but can be reactivated to help support normal immunity. Natural herbs like curcumin, turmeric, and resveratrol can help activate T-regulatory cells.

Decrease Exposure to toxins

It is important to decrease exposure and consume clean organic foods, clean air and filtered water from glass not plastic. Anything you put on the skin should also be as natural as possible. Avoid Phthalates and fragrances as they can be potential triggers as well.


If your immune system is overreacting, detox pathways should be optimized. The primary detox methods occur through kidneys/urine, stool (liver and gut), and sweat (skin). Optimizing these pathways with plenty of clean water and fiber is important. Also, supporting the detox pathways with essential vitamins and minerals is vital to minimize oxidative stress and provide a more homeostatic environment to calm the immune system. Antioxidants help with the oxidative stress that can occur with immune activity. Oxidative stress is a known trigger for cell death and potential immune activation.

Related post: How To Detox Your Body Naturally.

Final Thoughts

Being diagnosed with an autoimmune disease can be overwhelming. It is possible, however, to manage the autoimmune process and improve your quality of life through lifestyle changes.

While in this article we focused on natural options, it is important to note that certain medications can be profoundly impactful for autoimmune diseases. They do not always address, however, the underlying causes.

I hope you find this total-wellness approach to autoimmunity helpful. I wish you the very best success in your journey to a better health.

Read Next

Autoimmune Diet: Dr. Kessmann covers some of the key guidelines and considerations for the autoimmune diet including: the elimination diet, foods to avoid, foods to eat and supplements.

Dr. Jennifer Kessmann, MD, AIHM, IFMCP

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