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Functional Medicine Solutions For Autoimmune Disease

There are a record number of people being diagnosed with autoimmune diseases and even more suffering from autoimmune-like symptoms. The conventional thought on autoimmune conditions is that they are idiopathic (which means that the cause is unknown). 


In recent years, however, research has found that various factors can increase the chance of developing an autoimmune disease. Removing or resolving those factors can lead to remission or elimination of symptoms. 

Some of these factors include heavy metal toxicity, poor diet, poor sleep, stress, environmental factors, chemical toxicity, injury, or viral, bacterial, or fungal infections. 

Patients with autoimmune diseases should be heartened by this new body of research because it says that so much of how they feel is still in their hands. 

For over a decade, I have specialized in complex and chronic illness, and these findings confirm what I have found in my own patients.  There is so much that can be done to improve quality of life, reduce symptoms and restore the joy lost when an unyielding diagnosis is thrust upon them. 



This list is not exhaustive. These are just a few things that can cause autoimmune disease and autoimmune symptoms. Importantly, there are steps that can be taken to mitigate symptoms with each of these contributing factors. 






  • LONG COVID & COVID [4][5]







The information in this article and on this website are intended for informational purposes only and does not take the place of seeing a doctor and should not be used for the purposes of diagnosis.  If you are experiencing severe symptoms, have chest pain or trouble breathing, go to a hospital right away. Consult a doctor before beginning or stopping any medications or interventions. 

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Usually, when a person begins to have autoimmune symptoms, their first step is to go to their primary care doctor.  Sometimes they have a test at the doctor's office (usually a single test to confirm the disease the doctor suspects), and then they are medicated.

The goal of the primary care physician is simply to mitigate symptoms by administering steroids, anti-inflammatory drugs, pain medication, or immunosuppressant drugs.


These drugs temporarily stop the pain signal to the brain, suppress the immune system, and essentially shut off the ‘fire alarm’ of the body that is trying to tell you that something is wrong.  

There is usually no attempt to deal with the actual cause of the 'fire alarm' itself. The real problem is never addressed.


It is very common for patients with autoimmune symptoms to be given a non-specific autoimmune diagnosis, especially when they don't fit the diagnostic criteria for a specific disease.  'Autoimmune-like symptoms' is usually a catch-all term to explain a mysterious condition.  


Maybe this happened to you, you go to a doctor, and their initial basic workup reveals that 'you're normal and there is no reason for your symptoms,' so they label your symptoms as 'autoimmune in nature' and give you steroids and pain medications and send you on your way. 


The wrong diagnosis is always worse than no diagnosis at all, as a patient sometimes spends their entire life trying to make sense of and treat a diagnosis based on wrong information. 




One of the most damaging concepts in circulation is that autoimmunity is the body ‘attacking itself.’  I do not like this concept for a few reasons. 


First of all, It is not a biochemically accurate description of what is happening - autoimmune symptoms are caused by the body reacting to a perceived threat.  


The second reason is that it places the burden of responsibility on the patient. It is essentially the patient’s ‘fault’ since the patient's body is ‘doing this to itself.' Often, the patient experiences a sense of betrayal by their body as a result of this misclassification. 


The body does not intentionally harm itself; it is doing everything it can to survive and adapt to a hostile internal environment in order to protect you.


It is the functional medicine practitioner's job to identify what 'perceived threat' your body is reacting to, remove that threat, and restore normal autoimmune function. 



This is not a comprehensive list. Here are a few tests that provide a baseline for how your body is functioning. Restoring balance can result in a huge improvement in the overall quality of life for patients. 

  • Micronutrient Testing - reveals hidden deficiencies. The micronutrient test and the stool test are generally high on the list of priority testing.

  • Comprehensive Stool Analysis - by far the best test for the complete evaluation of the microbiome. Tells us what to strengthen and what 'roadblocks' hinder the body from fully healing itself. 

  • Complete Thyroid Panel - important even if your autoimmune disease is not directly related to your thyroid. A complete panel should measure free T3, free T4, TSH, reverse T3, ant-TPO, anti-TG, and iodine.

  • Hormonal Analysis - This can be done with urine testing, where metabolites are measured to determine someone's ability to detoxify estrogens. Saliva testing can be done to test sex hormones and adrenal hormones.

  • Mold Toxicity Testing - anyone with a history of significant exposure or current/suspected exposure should get this done. Mold toxins can adversely affect the nervous system and immune systems and perpetuate dysfunction for decades.  Freedom from mold often equals freedom from chronic illness. 

  • Environmental Toxin Testing - tests for chemical toxins present in the body.  This testing is very useful in finding the cause of unusual symptoms. 

  • Heavy Metal Toxicity Testing


  • Advanced Cardiovascular Testing 

  • Food Sensitivity Testing - can be useful at the beginning, but it is always best to address the underlying factors contributing to food intolerance symptoms. 

  • Dental Saliva Testing - evaluation of pathogenic bacteria contributing to gingivitis.  Since the gastrointestinal system is one long tube, many times, what's happening in the mouth can affect what's going on in the gut. 

  • Organic Acids Test - best tool we have for evaluating the inner workings of the metabolism, gut function, oxidative stress 


Every symptom is modulated by the brain. Meditation and other practices radically change how pain and other sensations are processed in your body and can reduce or eliminate symptoms altogether. 

  • Spring Forest Qigong - a type of qigong that was created specifically for improving health and reducing pain. It uses gentle movements, deep breathing, and visualization to achieve dramatic improvements in health. [9] [10] [11]

  • Dietary Changes - Many people rely upon strict diets to keep their symptoms at bay.  Sometimes diets like the Mediterranean diet can be very healthy and useful. Other times, patients can get stuck only eating 4 or 5 'safe' foods. This is when a diet becomes too limited, and investigation is needed to determine the cause of food sensitivities. Especially for sensitive patients, specific foods rather than pills are often the best way to get vital nutrients into the body. 

  • Circadian Timing - subtle changes like adding carbohydrates at certain meals or changing meal times can make a big difference in symptom severity. 

  • Breathing techniques like 'square breathing' can help you get into a relaxed state more often during the day. 

  • Neuroplastic brain training - these techniques are very powerful and can help your body reduce or eliminate chronic symptoms (even from the most persistent and severe pain). Great places to start are The Way Out by Alan Gordon and Alon Ziv as well as The MindBody Prescription by Dr. John Sarno. 


The correct supplementation can be life-changing for a patient.  However, this requires a knowledge of the root cause as well as the 'order of operations' of what needs to be treated when.


This is why self-treatment with herbs and supplements rarely achieves success and why working with a competent functional medicine practitioner can make all the difference.  Here are just a few of the many supplements that can make a big difference to a patient. 

Please do not self-treat with this list, as there are important caveats for any supplement. Often, there is a form, brand, order, and dosage in which to take even the 'best' supplements for you. 

  • ONE Multivitamin - Pure Encapsulations - a good quality multivitamin is important for everyone, particularly those with autoimmune symptoms or disease. This one is exceptional.

  • SPM Active - Metagenetics - specialized pro-resolving mediators work to resolve chronic inflammation. If you have histamine issues, this one is not the best one to start with. 

  • Antimicrobials are a must for those with autoimmunity disease or symptoms. Berberine (especially useful for those with hydrogen SIBO), olive leaf extract, and monolaurin are some used often.  We use these natural medicines for their combined antiviral, antibacterial, and antifungal effects. 


  • Chelated Magnesium - a mixture of magnesium malate, magnesium citrate, and magnesium glycinate 

  • Intestinal Lining Healers - Mega IgG 2000, Megamucosa, Leaky Gut Revive are used often. GI Revive and added magnesium (helpful for those with constipation). 

  • Probiotics - most people have co-existent issues with histamine. The only probiotic perhaps worth it in the beginning is probiota bifido but it is only useful in about 25% of cases when starting treatment.

The information in this article and on this website are intended for informational purposes only and does not take the place of seeing a doctor and should not be used for the purposes of diagnosis.  If you are experiencing severe symptoms, have chest pain or trouble breathing, go to a hospital right away. Consult a doctor before beginning or stopping any medications or interventions. 

Dr Brian Lum Dark Logo.png

It is often said to those with autoimmune symptoms that they will have an autoimmune disease for the rest of their life. The implication is that they will never feel healthy again.  

While they may technically carry that diagnosis, I have had patients enjoy near-complete health and feel better than they did before their diagnosis.

While no one can guarantee these results for everyone - there are hundreds of variables to consider - significant health improvements are common. 

Many of my patients had previously been told that their autoimmunity will progressively worsen on its own, there is nothing to do to slow down or reverse the damage caused by these symptoms, and the ONLY treatment is steroidal or anti-inflammatory medication - in the vast majority of cases, this is untrue.

There are many examples of successful treatment of autoimmune diseases through natural interventions.


Dr. Terry Wahls is an excellent example of a doctor who was diagnosed with progressive multiple sclerosis and reversed her illness using functional medicine and paleo principles. [12] She no longer uses a wheelchair.


There is a lot a patient can do on their own and with the help of a functional medicine practitioner to lessen pain, inflammation, and the overall severity of symptoms. 








A deep dive into a patient’s history and overall medical condition is necessary to determine the potential causes of autoimmune disease/symptoms as well as to map out a course of treatment. 


Often, the body is trying to rebalance itself from various underlying factors - like inflammation from seasonal allergies, work stress, mold exposure, and lingering Long Covid. 

The first step for any patient is to make sure they are getting a complete diagnostic assessment and utilizing testing that goes above and beyond the basics to identify in-depth clinical imbalances.



This would benefit patients who have not been diagnosed with an autoimmune disease but suspect they have one, as well as those who have unclassified 'mysterious' symptoms. 


A test proving you have a condition should be only the first step in your treatment. Your diagnosis alone gives you no information about how your body functions and what impediments may need to be removed for you to heal. 


Your body is unique, and you may not fit into a category easily.  You deserve to be taken seriously and not be told 'it is all in your head.'  Complex symptoms require a nuanced and thorough approach that a complete functional medicine evaluation can provide.  

Dr. Brian Lum is a certified functional medicine practitioner who has been treating patients with complex and chronic illnesses for over a decade. We offer remote online consultations for patients around the world. 



Disclaimer: If you think that you may have a medical emergency, call your doctor or 911 immediately. No action or inaction should be taken based solely on the contents of this information. Nor should you ever delay seeking medical advice or treatment due to the information contained on this Website. The information on this Website is not intended to diagnose, treat, cure, or prevent any disease or medical condition. The information discussed is not intended to replace the advice of your healthcare provider. Reliance on the information provided by this Website, Dr. Brian Lum, or Functional Healthcare Institute is solely at your own risk.


[1Parks, Christine G, Aline de Souza Espindola Santos, Catherine C Lerro, Curt T DellaValle, Mary H Ward, Michael C Alavanja, Sonja I Berndt, Laura E Beane Freeman, Dale P Sandler, and Jonathan N Hofmann. 2019. “Lifetime Pesticide Use and Antinuclear Antibodies in Male Farmers From the Agricultural Health Study.” Frontiers in Immunology 10: 1476–1476.

Parks, C.G., K.H. Costenbader, S. Long, J.N. Hofmann, Freeman L.E. Beane, and D.P. Sandler. 2022. “Pesticide Use and Risk of Systemic Autoimmune Diseases in the Agricultural Health Study.” Environmental Research 209: 112862–112862.

[2] Lieberman, Allan, and Luke Curtis. 2020. “Mold Exposure and Mitochondrial Antibodies.” Alternative Therapies in Health and Medicine 26 (6): 44–47.


[3] Boscolo, Paolo, Pierre Youinou, Theoharis C Theoharides, G Cerulli, and Pio Conti. 2008. “Environmental and Occupational Stress and Autoimmunity.” Autoimmunity Reviews 7 (4): 340–43.


[4] New Real-World Study Demonstrates Connection Between Long COVID and Rheumatic Autoimmune Disease Symptoms and Environmental Triggers. 2022. New York: PR Newswire Association LLC.


[5] Jacobs, Jeremy, and Quentin Eichbaum. 2021. “COVID‐19 Associated with Severe Autoimmune Hemolytic Anemia.” Transfusion (Philadelphia, Pa.) 61 (2): 635–40.


[6] Grankvist, Anna, Per-Ola Andersson, Mattias Mattsson, Monica Sender, Krista Vaht, Linnea Höper, Egidija Sakiniene, et al. 2014. “Infections With the Tick-Borne Bacterium "Candidatus Neoehrlichia Mikurensis" Mimic Noninfectious Conditions in Patients With B Cell Malignancies or Autoimmune Diseases.” Clinical Infectious Diseases 58 (12): 1716–22.

[7] Cutolo, Maurizio, Carmen Pizzorni, and Alberto Sulli. 2011. “Vitamin D Endocrine System Involvement in Autoimmune Rheumatic Diseases.” Autoimmunity Reviews 11 (2): 84–87.


[8] Macarenco, Maria-Magdalena, Cristian Opariuc-Dan, and Cătălin Nedelcea. 2021. “Childhood Trauma, Dissociation, Alexithymia, and Anger in People with Autoimmune Diseases: A Mediation Model.” Child Abuse & Neglect 122: 105322–105322.


[9] Sawynok, J., & Lynch, M. E. (2017). Qigong and Fibromyalgia circa 2017. Medicines (Basel, Switzerland), 4(2), 37.

[10] Vincent, A., Hill, J., Kruk, K. M., Cha, S. S., & Bauer, B. A. (2010). External qigong for chronic pain. The American journal of Chinese medicine, 38(4), 695–703.

[11] Coleman J. F. (2011). Spring Forest Qigong and chronic pain: making a difference. Journal of holistic nursing: official journal of the American Holistic Nurses' Association, 29(2), 118–131.

[12]Wahls, Terry L., and Eve Adamson. 2014. The Wahls Protocol : How I Beat Progressive MS Using Paleo Principles and Functional Medicine. New York: Avery, a member of Penguin Group (USA).


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