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Autoimmune Disease

Updated: Apr 25, 2020

The National Institutes of Health estimate that 5-8% of Americans have an autoimmune disorder. There are approximately 80 human diseases caused by an autoimmune response and that list keeps getting longer. Autoimmune disease occurs when our immune system attacks our own tissues by mistake. This can escalate and lead to tissue destruction such as the joint tissue destruction in Rheumatoid Arthritis. Goals of Naturopathic treatment are to modulate the immune system, address any dysbiosis (imbalance in the microbiome), reduce inflammation, address hormonal imbalances, address stress and the psycho emotional aspect, optimize nutrition and address detoxification if appropriate. Some of the causative factors we look at in autoimmune disease include molecular mimicry, the microbiome, intestinal permeability, nutritional status, environmental triggers, genetics and stress.

Molecular mimicry: This is a critical piece to autoimmune disease. The basic concept is that your body mounts an immune response to something (pollen, food, virus, bacteria, etc.) and then those immune cells become confused and start attacking your tissues. Klebsiella has been associated with ankylosing spondylitis and ulcerative colitis; Yersinia has been associated with autoimmune thyroid conditions; Citrobater has been associated with rheumatoid arthritis to name a few. Association isn’t causation but it warrants investigation especially into the microbiome of patients with autoimmune disease.

Microbiome: We have trillions of microorganisms (bacteria, viri, parasites) living in our intestinal tract. This is called the microbiome or gut microbiota. Your microbiome starts to develop the moment you are born and complete colonization occurs within the first three years of life. Starting at birth, our microbiome helps train the developing immune system. The commensal (good) microbes can directly attack the disease causing microbes signaling to the human immune system when to launch an attack. This training also includes teaching the immune system to ignore harmless stimuli (such as pollen or even self tissue). Without this critical training we are more at risk for conditions such as autoimmune disease and allergies.

Intestinal permeability: This goes hand in hand with molecular mimicry and the microbiome. Intestinal permeability is often called “leaky gut”. Our GI tract is technically outside of our body, you could eat a penny and it would pass right through your GI and out into the stool. Your body determines what is brought in through the GI tract into your bloodstream. When there is a breakdown in this process and larger particles are allowed in to the blood we call that intestinal permeability. When larger strings of amino acids (pieces of food that aren’t entirely broken down) make it through, the body attacks these as foreign invaders (as it should!). This attack can go awry and lead to attack on your own bodily tissues. Intestinal permeability is caused by stress, poor diet, overuse of NSAIDS, alcohol and more.

Genetics: Depending on the autoimmune condition there may a stronger or weaker genetic link or family history. A number of genes have been implicated in causing autoimmune disease especially genes related to HLA. Your genetics are not your destiny. Research on epigenetics (turning genes on and off) is fascinating. Your lifestyle and diet play a major role in epigenetics.

Treatment is always tailored to the patient and includes dietary changes with an emphasis on a high antioxidant diet rich in vegetables. We also work to help balance the immune system by using herbs and supplements. One part of working on this immune reaction is getting to the bottom of what caused it with helping to heal any intestinal permeability and balance the healthy flora in the GI tract.

Mind body medicine is critical for autoimmune disease. We must analyze stressors, stress response and any somatic manifestations of that stress. Research around adverse childhood experiences (ACEs) and mind body medicine is striking and incorporated in to patient care.

It is important to maintain all medications while working on your health from a holistic perspective. Autoimmune disease is serious and tissue destruction is permanent. Our goal with naturopathic treatment is to keep the medication dose stable and slow or stop the autoimmune destruction. I am often asked if patients can expect to stop their medication eventually and that depends on a variety of factors and is a decision made with the prescribing practitioner and patient.

If you are struggling with an autoimmune disease I recommend working with a naturopathic doctor to help identify the root cause and support your body.

I offer group classes to provide financially accessible care and enhance the therapies with community support. Click here for more information on my autoimmune group program.

*The treatment discussion in this article is simplified and meant for educational purposes only. Please consult with a naturopathic doctor before implementing changes to your treatment plan.


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