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A Functional Approach To Autoimmune Disease

Written by

Deborah Freudenmann BHSc

The root cause of all autoimmune diseases is the same: your immune system, which is supposed to protect you from invading microorganisms, turns against you and attacks your cells instead. Depending on which cells or proteins are attacked, this determines the type of autoimmune disease.

Recent years have witnessed a sharp rise in the incidence of autoimmune conditions possibly due to the increased exposure to factors that can trigger the development of these diseases.

The vast majority of autoimmune diseases are chronic. These conditions tend to progress over a period of time resulting in considerable damage to healthy tissues.

People who suffer from one or more autoimmune diseases often feel helpless, slaves to their disease, and powerless to improve their health.

Hence, there is a need to understand the role of factors that can trigger the development of autoimmune diseases and the right ways to protect yourself from the serious complications associated with them.

Functional medicine offers a unique approach to the management of autoimmune disorders. It is different from the treatment methods adopted by conventional or standard medicine as it aims to identify and eliminate the root cause of autoimmune disorders instead of just relieving the symptoms.

Read on to learn more about autoimmune disorders and how functional medicine can provide effective solutions for controlling these conditions.

Understanding autoimmunity

The primary function of our immune system is to protect us against infections, and other harmful substances such as toxins, pollutants, and irritants.

The immune system of the body develops according to the external environmental factors you are exposed to and your genetics. The early immune response is largely dependent on the transfer of the antibodies from the mother to the baby until the infant is strong enough to develop their own immune response.

Autoimmunity refers to an abnormal response of the immune system, which occurs when the immune cells mistakenly attack and damage the body’s own tissues. This abnormal response is the result of the failure of the immune system to recognize the body’s tissues as its own.

So, the immune cells consider the healthy tissues as foreign bodies that must be destroyed.

Hence, it stimulates an immune response that is similar to the one that is triggered for fighting infections or toxins.
However, this form of response against the body’s own cells results in the destruction of these tissues.

For example; when the immune cells consider the thyroid tissues as foreign bodies, they may attack and destroy the gland due to which patients may develop Hashimoto’s disease.
Similarly, rheumatoid arthritis develops when the immune cells attack and destroy the healthy tissues of the bones and joints considering them to be harmful to the body.

Some other examples of autoimmune disorders include lupus, type 1 diabetes, coeliac disease, scleroderma, Graves disease, multiple sclerosis etc.

The treatment of autoimmune disorders should be aimed at identifying the factors that trigger the immune system causing it to mount such as abnormal response against the healthy organs.

Read on to find the top 10 common causes of such an abnormal immune response and the right ways to avoid them in order to prevent the development and slow down the progress of autoimmune disorders.

1. Abnormal gut flora

The health of your gut determines what nutrients are absorbed and what toxins, allergens and microbes are kept out, and therefore it is directly linked to the health of the total organism.

A weak gut flora that lacks diverse strains of healthy bacteria can contribute to the development of autoimmune disorders. It can increase your risk of leaky gut syndrome, intestinal dysbiosis, and microbiome imbalances. Gut bacteria support our immune system and when these bacteria are consistently destroyed our first immune response to disease also gets destroyed.

Leaky gut syndrome causes the intestinal lining to become inflamed and the microvilli to become damaged or altered. The damaged microvilli then cannot produce the necessary enzymes and secretions that are essential for a healthy digestion and the absorption of nutrients.

As the damage progresses to the tight junctions, the gaps become wider and wider allowing unwanted particles into the bloodstream. Damage to the intestinal tight junction barrier followed by the invasion of harmful substances leads to inflammation. This provokes the immune system to produce antibodies to fight off the molecules, as they are perceived as antigens.

Research has shown that there is a higher correlation of intestinal permeability to
autoimmune disease due to a combination of inflammation, dysbiosis and genetic predispositions. Intestinal permeability or leaky gut reduces absorption of nutrients essential for cellular function, detoxification, brain function, tissue repair, decreases energy, mood, cognitive function and gut repair.

2. Food sensitivities

Food sensitivities can trigger your immune system resulting in the activation of the immune system. Eliminating the foods that can cause inflammation in your gut is one of the best ways to inhibit abnormal immune response and prevent the progress of autoimmune disorders.

In autoimmune conditions, gluten and dairy are very common and prominent causes and contributing factors. Thus, avoiding gluten and dairy is highly recommended.

You can maintain a food diary and note down the foods you eat on a daily basis. Correlating the information about your diet with the occurrences or exacerbations of your symptoms like joint pain, stuffiness, skin rashes, and itching would help you identify the possible food triggers.

Once you have identified these foods, you can avoid their consumption to protect yourself against autoimmune disorders.

3. Nutritional deficiencies

Deficiency of nutrients such as vitamin D, zinc, vitamin C, Glutathione, and healthy fats like omega 3 fatty acids can affect the functions of the immune systems.
These deficiencies may occur due to the lack of nutrients in your diet or poor digestive functions due to which the breakdown, assimilation, and absorption of nutrients in the intestine are affected.
Ensuring your diet comprises all the essential vitamins, minerals, and other nutrients needed for the optimum functioning of the immune system is the key to preventing autoimmune disorders.
You can also make efforts to restore healthy gut functions by limiting your sugar intake and improving gut flora in order to ensure these nutrients are absorbed into your body efficiently.

4. Chronic inflammation

Chronic inflammation is often at the root of autoimmune disorders. Chronic inflammation can occur as a result of a combination of factors including hormonal imbalances, mental stress, nutritional deficiencies, poor gut flora, food sensitivities, toxins and latent infections.
Identifying these causes and reducing your exposure to them would minimize inflammation and reduce your risk of developing serious complications linked to autoimmune disorders.

5. Immune system dysregulation

Immune system dysregulation may occur due to inflammation and oxidative stress caused due to free radical damage.
The use of natural anti-inflammatory and antioxidant agents like glutathione, vitamin C, and curcumin may reduce or reverse these changes and restore healthy immunity thus protecting you from autoimmune disorders.

6. Chronic infections

Infections caused due to bacteria, fungi, viruses, or parasites can trigger an abnormal response of the immune system triggering the development of autoimmune disorders.

For example; intestinal dysbiosis caused due to the overgrowth of harmful bacteria, parasites, and fungus in your gut microbiome can put you at risk of developing autoimmune disorders.

Similarly, leaky gut and SIBO (small intestinal bacterial growth) are common factors that can contribute to the development of autoimmune diseases like inflammatory bowel disease, celiac disease, scleroderma, and Hashimoto’s hypothyroidism.

7. Toxic exposure

Exposure to toxins like chemicals, air pollutants, cosmetics, and additives and preservatives in foods can create an adverse impact on our immune system resulting in chronic inflammation, and oxidative stress.

Avoiding the use of chemical-based cosmetics and eating freshly cooked meals at home are some ways to minimize your exposure to harmful toxins and prevent the development and progress of autoimmune diseases.

8. Hormonal imbalance

Imbalances in the production and release of hormones like insulin, estrogen, progesterone, and testosterone can contribute to inflammation and worsen your risk of autoimmune disorders.

The inflammatory insulin surge is more common in patients with diabetes, though it may occur even in healthy individuals. It is advisable to minimize your intake of sugars to prevent insulin surges that could otherwise worsen inflammation as well as insulin resistance.
Maintaining hormonal balance can also restore healthy immune system functions and prevent the risk of autoimmune disorders.

9. Chronic stress

Chronic stress can contribute to inflammation and immunological disturbances. Chronic stress also leads to hormonal imbalances by creating disruptions in the levels of stress hormones like cortisol and feel-good hormones like dopamine and serotonin. It may also worsen nutrient depletion.

Addressing factors that cause stress can be a great way to avoid these triggers and protect yourself against autoimmune disorders.

10. Emotional trauma

Emotional trauma is a common cause responsible for the relapse and frequent exacerbations of the symptoms of autoimmune disorders.

Adopting stress-relieving methods like yoga, meditation and deep breathing would help you face difficult life situations with better ease and confidence allowing you to avoid the repeated episodes or exacerbations.

Functional medicine approach for detecting the root cause of autoimmune disorders

Your functional medicine health coach or practitioner would analyze your symptoms and correlate them to a number of factors including your diet, your family history, and the kind of stress you are experiencing, to identify the possible trigger.

Some tests may be recommended to confirm or rule out the possible triggers.

The commonly recommended tests for the detection of triggers for autoimmune disorders include:

  • Compressive blood count tests such as CBC with differentials
  • Hormonal tests to check the levels of estrogen, progesterone, insulin, and testosterone
  • Thyroid hormone tests for measuring the levels of thyroid hormones
  • Test for the detection of Hashimoto’s antibodies, especially if Hashimoto’s thyroiditis is suspected
  • Comprehensive stool analysis including microbiome testing
  • SIBO breath test for the diagnosis of gut-related issues
  • Nutritional tests to measure the levels of vitamins, minerals, healthy fats, antioxidants, and amino acids for the diagnosis of nutritional deficiencies
  • Salivary adrenal and cortisol function tests to evaluate stress-linked hormonal disturbances
  • C-reactive protein (hs-CRP) to assess the extent of inflammation
  • Methylation and homocysteine status for identifying issues related to these processes
  • Tests to identify allergens and food sensitivities


Autoimmune disorders can be treated more effectively by identifying and eliminating the root causes responsible for the same. The functional medicine approach provides a comprehensive way to detect the factors that can contribute to the development and progress of autoimmune disorders.

Functional medicine also has the potential to heal the immune system and allow you to follow a proactive and personalized approach to improving your health and wellness.

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  • 3 Responses

    1. Dear Deborah,

      I have enjoyed your posting about FM approach to Autoimmune diseases. It’s very eye opening.
      I have got a client, suffering from Multiple Sclerosis. He is now on Wheel Chair because all his lower limbs cannot longer support him. Can this condition/stage of MS still be reversible? If yes. Where do we start from? I know you have listed all the tests that need to be done. But I still would need your input.

      Mike Ogwal (a Functional Medicine Candidate)

      1. Hello Mike,

        I appreciate the comment. It’s beautiful to hear that the article could provide some insight to understanding some of the causes for autoimmune disease.

        With any stage of chronic degenerative disease or progressive autoimmune disease, we aim to slow down and halt progression. Depending on the damage and state of health, once addressing root causes there is always the possibility of healing. Not to mention, alleviating some of the discomfort and constant struggle of various symptoms.

        With MS, there are a few causes that stand out and I would address first (of course this is theoretical without evaluating the client myself)


1. Leaky gut and a distorted gut microbiome. I would remove all gluten and dairy from the diet and work on reparing the gut microbiome.
        2. Mycotoxin exposure and heavy metals such as copper, cadmium, mercury, lead and iron. This is commonly found in autoimmune diseases which impact the central nervous system. Addressing a mould exposure and/or heavy metal toxicity would be a priority. If either is the case, supporting the detoxification pathways etc.
        3. Are there any latent infections? Such as herpes simplex virus or epstein-Barr virus. Or toxins produced by bacteria such as: M. pneumoniae, C. pneumoniae, and C. perfringens. Something to consider.
        4. Replenishing nutrients that are depleted such as B vitamins, magnesium, selenium etc..
        5. Supporting the immune system with nutrients such as vitamin D and glutathione…

        Just a few thoughts… Each and every client is unique and each autoimmune presentation is individual. Thus, some factors may not be relevant whereas the mental component and infections may be the most prevalent in another client.

        I hope this gives you a little insight on how to support your client further.



    2. I enjoy your posts but note the absence of references. When you mention “studies” please provide the reference. Thank you

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