The Naturopathic Approach to Treating Autoimmune Disease

Autoimmune disease is defined as an immune reaction against one’s own tissues [1]. A robust immune system needs to fight foreign invaders but not harm ourselves in the process. A large proportion of the Canadian population are diagnosed with these conditions. We now know more than ever about autoimmune disease and all the contributing factors. A naturopath can take the time to identify all the factors and help you deal with your condition from a wholistic perspective. 

Conventional medicine generally addresses autoimmune disease in an effective, yet limited way. Drugs tend to focus on one aspect of this whole process, whereas, autoimmune disease must be viewed as a multi-factorial condition. 

In my clinical practice, we focus on the following when treating any autoimmune disease. 

  1. Immune Function
  2. Gut health 
  3. Addressing the basics of Genetics and Epigenetics.
  4. Hormone Health 

Immune Function 

The immune system is a priority in treating any autoimmune disease. Most conventional doctors will focus on the autoimmune disease by prescribing specific immune inhibiting medications. In most cases patients aren’t educated on other ways we can control the immune system. 

The immune system is intimately related to nutrition; proteins, vitamins and minerals combine to make our immune cells. Also, our digestive tract and immune system work in close relation. In fact, about 70% of our immune system lies in the gut. Therefore, gut health must also be considered in assessing immune function. Certain foods can contribute to immune over-activation (a bad thing). 

Furthermore, numerous botanical medicines which can modulate the immune system. Human clinical data has demonstrated specific herbs can be beneficial for specific autoimmune conditions. 

Naturopaths can combine nutrition, herbal and nutrient supplementation to modulate your immune system and consequently autoimmune disease.   

Gut Health 


The gut has many mechanisms to ensure beneficial intestinal bacteria. Bacteria is important as they influence the immune system, affect our genetics and contribute directly to autoimmune disease. 

There is evidence of altered gut bacteria in most autoimmune diseases including: Inflammatory Bowel Diseases, Multiple Sclerosis, Type 1 Diabetes, Guillian-barre, Fibromyalgia, Lupus , vasculitis, psoriasis, eczema and Rheumatoid arthritis [3].

This is significant because naturopaths have many ways to help, including supplements (such as specific probiotics) [22] and prebiotics. Dietary change can also benefit the gut bacteria and autoimmune disease [1]. 

Intestinal Permeability (aka Leaky Gut)

For decades, the concept of leaky gut was refuted, but now, finally, there is an abundance of scientific research showing leaky gut is real and can contribute to autoimmune disease and other diseases. 

The gut is sophisticated, with our immune system and digestive tract intimately connected. If we have dysfunction in the immune system, the gut can be impaired, and conversely, an altered gut lining can harm the immune system. 

There are several ways a gut can become leaky, including many dietary factors [3], aging [7], stress [3], alcohol consumption [3], gut infection [5], and inflammation [9]. 

It’s promising because there are many supplements useful in treating leaky gut. Things like gut bacteria, vitamins and minerals and specific amino acids can be used in combination to address the gut. 

Your naturopath can learn a lot about your gut health by taking a detailed health history. Understanding your day to day symptoms and digestive function tells a lot. Functional stool testing can also be helpful. Some tests can show markers of inflammation, leaky gut, bacteria and enzymatic activity within the gut. More can be learned about the Comprehensive Stool Analysis here. 


Most people are familiar wit the idea autoimmune diseases are genetic conditions, that’s why they tend to run in the family. Although we cannot change our genes, we now know how much our environment can influence our genes. Genes can turn on or turn off based on our environment.  Keep this in mind: 30% of autoimmune disease arises from genetic factors, whereas 70% comes from environmental factors. Don’t get caught up on the fact it runs in the family, our day to day lives matter the most!

 This concept is called epigenetics: our genes are influenced by our environment. 

Toxins [5], medications [7], certain infections [8], diet and stress are just a few things known to trigger our genes to present with autoimmune disease. 

A naturopath cannot claim to change your genes, but we can certainly help optimize your environment to favour the best genetic makeup. 


It’s said about 10% of the population suffers from autoimmune disease, but 78% of those are women [1]. A lot of symptoms also tend to vary based on menstrual cycle (including pregnancy). These factors tell us sex hormones (namely estrogen) have lots to do with autoimmune disease. 

Not only does autoimmune disease see this difference based on hormones. Immune function in general. When females are immunized, they produce more antibodies than males[1], and this was proven to be due to their estrogen levels. 

How can we control hormones? Well hormones themselves can be good or bad. Estrogen for example, exists in 8 different forms, of which some are good and some are bad. The bad ones tend to relate to autoimmune disease [5]. 

A naturopath can help focus on hormone health and conduct more in depth hormone testing. We have a wide range of botanical medicines, vitamins, minerals and nutrients which can be used to optimize hormone health. 

Treating Specifics 

Once the general influences like immune function, gut health, hormones and epigenetics are taken care of, we can also target your specific autoimmune condition. 

If a person has autoimmune joint disease versus autoimmune thyroid disease, our treatment will vary. We have a targeted approach to treating autoimmune disease too. Not every case presents the same, and a naturopath will be able to figure out the best treatment plan for you, for long term health. 



Autoimmune disease is a multi-factorial condition. An emphasis must be placed on immune function, gut health, hormones and genetics. Focused treatment also exists, where we take a patient’s specific case and presentation, and together come up with a comprehensive treatment plan. 

Conventional medicine tends to underserve the autoimmune population, with emphasis on the immune system alone. A naturopath can teach you a lot about your condition and all the contributing factors.

Please click here to book in for an initial assessment with Dr. Johann de Chickera to learn more. 

Dr. Johann de Chickera

Dr. Johann completed his 4-year degree at the Canadian College of Naturopathic Medicine, in Toronto. His clinical focus lies in chronic disease, such as those related to the Gastrointestinal, Endocrine, and Immune Systems. 

Johann joined Body Co. in 2019, with enthusiasm and desire to joint a forward thinking, integrity driven and results-based multi-disciplinary clinic. Having worked alongside physiotherapists, massage therapists, osteopaths and other health care providers, he is confident he will complement the current providers and help maximize new and existing patients’ overall care.

His approach to medicine relies on working with the patient to come up with a feasible, multi-factorial approach that addresses all complaints at once. He employs a strong background in diagnostic medicine and human physiology and pathology to diagnose and treat. His treatment involve a combination of nutritional counselling, botanical medicine, eastern medicine (acupuncture), nutraceutical supplementation and hands on physical medicine. 



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