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Complementary and Integrative Medicine for The Treatment of Autoimmune Diseases

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Complementary and Integrative Medicine for The Treatment of Autoimmune Diseases

In 2021 23.5 million people in the United States had an autoimmune disease, with prevalence rates expected only to increase. Moreover, there are at least 80 different types of autoimmune diseases. While many factors are involved in their etiology, determining the underlying root cause of these conditions can help better understand how to improve the quality of life of those affected.


What is an Autoimmune Disease?

An autoimmune disease is when the body's immune system attacks its own tissue, as it mistakes it for foreign and, therefore, not part of the body or “self”. This results in an autoimmune reaction characterized by the presence of antibodies and is referred to as molecular mimicry.

While the exact mechanisms are not entirely understood, a combination of bacteria, viruses, and toxins are thought to play a role. Leading to inflammation in the body and provoke an autoimmune reaction, as indicated by elevated levels of antinuclear antibodies (ANA).

ANA are antibodies or proteins the immune system produces to fight off foreign substances or invaders. However, antinuclear antibodies (ANA) instead attack one's own healthy cells and tissues, wreaking havoc on the body.

As noted, over 80 identified autoimmune conditions include Graves, Hashimotos, Type 1 Diabetes, Irritable Bowel Disease (IBD), Fibromyalgia, Lupus, and Chrohns, among others.

Autoimmune Disease Symptoms

The symptoms of autoimmune disease are numerous and include the following:

  • Fatigue
  • Joint pain
  • Weight gain and difficulty losing weight,
  • Anxiety
  • Depression,
  • Low libido
  • Abdominal pain
  • Digestive issues
  • Systemic Inflammation

What Causes Autoimmune Disease?

The etiology of autoimmune disease is various and multifactorial, including several genetic and environmental factors. Let's dive into some of the underlying causes of autoimmune disease.

Genetic Predisposition

While genetics is an important factor in the etiology of autoimmune disease, as they can make one more susceptible, they are only one piece of the puzzle. As the saying in Functional Medicine goes: “genes load the gun, and the environment pulls the trigger”- highlighting the environment's role in developing autoimmune diseases (1).

Environmental Toxins

Environmental toxins such as heavy metals and toxic solvents such as benzene from chemical plants can contribute to autoimmune conditions by inducing epigenetic changes, particularly for those with genetic susceptibility, by causing immune dysregulation and inflammatory responses.


Stress is a significant contributing factor to Autoimmune conditions. While genetic predispositions can make one more prone to an autoimmune disorder, chronic stress can “pull” the trigger. In fact, there is emerging research highlighting this fact by looking at the role that psychological stress plays in autoimmune disease. High rates of comorbidities between Post Traumatic Stress Disorder (PTSD) and autoimmune conditions have been found, highlighting how chronic stress can cause inflammation as well as alterations in the HPA axis.

Intestinal Permeability

Intestinal permeability or leaky gut can further contribute to systemic inflammation, malabsorption, and gut microbiome imbalances, all of which can contribute to autoimmune disease.

Gut Microbiome Imbalances

The gut microbiome is the epicenter of health, including immunity. When the gut microbiome is out of balance due to conditions such as dysbiosis, this can result in imbalances in the beneficial bacteria in the gut and cause imbalances in the immune system. The composition of the gut– including the diversity of bacteria, the ratio of beneficial to pathogenic bacteria, and how bacteria respond to the host— are all examples of gut microbiome imbalances that can impede immunity.

Systemic Inflammation

Systemic inflammation or silent inflammation can ensue due to microbiome imbalances stemming from a leaky gut, and immune system imbalances. Inflammation can play a role in the body's natural immune response and could lead to the development of autoimmune disease.

Imbalance in The Immune System

As noted, a hallmark of Autoimmune Disease is when the body attacks healthy tissue as it perceives it as foreign and not part of “self”. This imbalance in the immune system causes systemic inflammation in the body, which further contributes to autoimmunity. This results in a cascade response of self-perpetuating inflammation, leading to significant tissue damage. The exact mechanism for inflammation in autoimmunity is due to abnormal or disrupted T-cell response.

Hormonal Imbalances

Thyroid function is imperative for our overall health, including our gut microbiome and immunity. Chronic stress and inflammation can cause alterations and dysregulation in the HPA axis, leading to hormonal imbalances and impeding upon the thyroid, which can further wreak havoc on immunity. Thyroid health has been associated with autoimmune disease. This is because thyroid function is necessary for the body to work efficiently and to regulate processes relative to immunity. The thyroid is especially vulnerable to autoimmune conditions.

Functional Medicine Labs to Test for Root Cause of Autoimmune Disease

There are a number of functional medicine labs to evaluate the root cause of autoimmune disease. Testing is important as it allows the practitioner to see the whole picture of the individual– just like different pieces of a puzzle– so that they are able to pinpoint what is at the root of the autoimmunity.

Functional labs may consist of the following:

Comprehensive Stool Test

The gut microbiome is at the epicenter of autoimmunity. This test is important as it provides a comprehensive overview of the bacteria that reside in the gut microbiome regarding diversity, composition, and how the bacteria respond to the host. Furthermore, this test detects infectious parasites and pathogens.

Anti-Nuclear Antibodies ANA

This test assesses for antibodies that can be indicative of autoimmune disease. A positive ANA test means autoantibodies are present, and further lab work for autoimmune disease would likely be performed.

C-Reactive Protein (CRP)

This test evaluates inflammation. A high CRP can be a marker for inflammation and immune activity and help screen for autoimmune disorders.

Comprehensive Thyroid Panel

Getting a comprehensive Thyroid Panel is important as many autoimmune conditions such as Hashimotos or Graves target the thyroid.

Food Sensitivities/Food Allergies

Food allergies or sensitivities are imperative to assess for as they can provide insight to what is triggering the body, including the gut and immune system as nearly 80% of the immune system is housed in the gut.

Intolerances to gluten, dairy or other foods can contribute to symptoms of inflammation, alter gut composition, and wreak havoc on the immune system.  

Toxin Exposure

This test evaluates toxic exposures from one’s environment with a simple urine sample which can provide insight to an underlying causal factor to Autoimmune Disease. Toxins from one’s environment can impede upon the thyroid, immunity and the functioning of the gut– all of which contribute to autoimmunity.

Micronutrient Testing

Nutritional deficiencies are often apparent in those with autoimmune disease due to malabsorption factors. Therefore, ensuring one is sufficient in all the vitamins and minerals that are important in supporting their body, especially in dealing with autoimmunity, is imperative.

Genetic Testing

This test provides insight into a number of measures of our health related to inflammation, detoxification, and hormones. This data improves knowledge of how one's body systems functions based on their unique genetic make-up, what conditions they may be more susceptible to, and the areas that could use the most focused support.


This test measures antibody responses to 7 of the most common infections associated with autoimmune nervous system conditions.


Complementary and Integrative Medicine Options for Treating Autoimmune Disease Naturally

Functional Medicine offers many options for treating autoimmune diseases naturally. Once testing identifies the root cause of autoimmune disease, you can begin to treat the root cause of it. Natural approaches to treating autoimmune disease consist of the following:

Address Gut Microbiome

Triggers may include sugar, wheat, processed foods, dairy, and gluten. Among other intolerances one may have. Repairing the gut with amino acids such as L-Glutamine may be recommended.

The 5 R Protocol may also be recommended depending on individual needs. This diet consists of removing what is disruptive to the gut. Replacing with digestive enzymes, HCL, or bile that one may be deficient in. Reinoculating with probiotic-rich food sources and nutrient-dense foods. And finally, repairing the gut lining with supportive nutrients such as glutamine.

Rule Out Food Allergies and Sensitivities

Food allergies and sensitivities can impede upon the integrity of the gut lining and lead to systemic inflammation, gut microbiome imbalances, and malabsorption—- and contribute to autoimmune conditions.

Manage and Reduce Stress

High levels of chronic stress can cause imbalances in the immune system and the gut microbiome. Stress can reduce stomach acid in the gut, impede microbial diversity and composition, and contribute to intestinal permeability or leaky gut. Moreover, repeated stress can cause inflammation and wreak havoc on immunity.

Reduce Toxin Exposure

Toxic exposure from the environment can cause oxidative stress and inflammation in the body and wreak havoc on immunity. You can reduce exposure to environmental toxins by using an air and water filter, fragrance-free and natural household cleaners, and switching from plastic to glass storage containers.

Rule out Infections

Infections occur when viruses, bacteria, or other microbes enter the body and multiply. The body's response to infection often results in redness, inflammation, and fever. Infections can trigger autoimmune disease, especially for those with genetic predispositions. If you suspect you have an infection, it's important to seek medical attention to rule this possible cause out.

Autoimmune Disease Diet

A significant body of research indicates that plant-based, anti-inflammatory, and whole foods diets may support autoimmune disease.

Research suggests that nutritional approaches with characteristics of both a Mediterranean diet and one rich in whole foods and unprocessed meats have effectively supported autoimmune conditions.

Both ways of eating favor eliminating ultra-processed foods while incorporating increased amounts of phytonutrients that help modulate immune function and reduce systemic inflammation, such as fruits and vegetables and locally caught seafood.

The Autoimmune Protocol Diet (AIP) is a type of functional medicine approach to autoimmune disease that is a more restrictive diet than the Mediterranean or other types of plant-based diets. The AIP diet focuses on “resetting” the gut and reducing inflammation by eliminating foods that can trigger the system while increasing nutrient-dense foods to support the body.  

Foods that are encouraged in the AIP diet include organic and local meats such as seafood, venison, poultry, grass-fed organic meat, herbs and spices, non-dairy fermented foods, bone broth, artichoke, parsnips, green tea in addition to organic fruits and vegetables.

Supplements and Herbs That Support Healing from Autoimmune Disease

Many supplements can support the body in healing from autoimmune diseases. Most of these supplements boost the immune system and provide as much support for the body to heal itself as possible.

Vitamin D

Vitamin D is imperative for immune function as well as to modulate inflammation— all of which are related to autoimmune disease. In this randomized, double-blind trial of 123 participants with confirmed autoimmune disease, Vitamin D supplementation over the course of 5 years was found to reduce autoimmune disease by 22%.

Omega 3s

Omega-3 fatty acids have a strong role in reducing inflammation as well as modulating immunity and have been indicated to have a role in supporting autoimmune conditions by downregulating inflammation. Studies have shown Omega-3’s role in improving the quality of life in patients with Multiple Sclerosis by reducing the rate of relapse times and reducing inflammatory markers.


Zinc is a trace element that is consumed through dietary sources with 15% of people in developed countries not meeting the recommended intake levels. Zinc modulates gut functioning, inflammation, and immunity having a supportive role on the immune system, and has been shown to help with autoimmune conditions like rheumatoid arthritis and Chron's disease.


Research indicates that glutamine can help to restore the gut barrier- helping to support intestinal permeability as well as reduce inflammation— having implications for autoimmune conditions. Glutamine is considered one of the most crucial nutrients for the healing of intestinal permeability or leaky gut, as it is the preferred fuel for intestinal cells.


Curcumin, a compound found in the spice Turmeric, has been found to support intestinal permeability or leaky gut, while modulating inflammation and supporting gut microbiome balance. All of these functions support autoimmunity. Overall, Curcumin supplementation was found to downregulate inflammation in those with autoimmune conditions with no adverse side effects.


Probiotics help in reallocating the gut with healthy, beneficial bacteria. This supports reducing inflammation in the system and therefore enhancing immune function. Probiotics can also strengthen the gut barrier, which can help to prevent toxins, pathogens, and undigested food particles from leaking into the bloodstream, which can further wreak havoc on the system.

Yoga, Chiropractic, and Acupuncture to Support Healing from Autoimmune Disease

Because stress can significantly contribute to autoimmune disease, complementary and integrative medicine (CIM) approaches may be of considerable value in modulating and improving symptoms.

Yoga: is a mind-body practice that involves intentionally moving the body into different poses and has been found to increase vagal tone, decrease inflammation and support gut functioning and nervous system health— all of which can be beneficial to those with autoimmune disease. In fact, in this 2019 randomized controlled study of 72 Rheumatoid Arthritis (RA) patients, it was found that those who participated in 8 weeks of yoga, noted a significant improvement in their symptoms as evidenced by a reduction in several inflammatory markers.

Chiropractic: treatment addresses misalignments in the spine. This form of CIM may support autoimmunity by promoting the nervous system and immune health while reducing inflammation. Chiropractic treatment helps in relieving the pressure on the nervous system by promoting the health and function of the cells, tissues, and organs governed or controlled by it. This form of treatment has also been found to stimulate the vagus nerve, increase relaxation, and release neurotrophins such as brain-derived neurotrophic factor- BDNF- promoting anti-inflammatory benefits while also supporting nervous system balance— all of which can support those with autoimmune disease.

Acupuncture: using thin needles at strategic points of the body to elicit beneficial physiological effects, has been suggested to support the modulation of the immune system through stress-relieving properties and reduce systemic inflammation– which has been proposed as an underlying mechanism in autoimmune disease. Therefore, acupuncture may be a valuable treatment for those with these conditions.



While the etiology of autoimmune disease is complex and multifaceted, many treatment options can prevent further damage from taking place. By addressing autoimmune disease from an evidenced-based, root-cause perspective, providers are empowering patients to work with their body's natural immune system to find symptomatic relief naturally.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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