Logo NHC

Autoimmune Disease: Root Causes and Key Strategies

autoimmune disease
Autoimmune disease is a condition in which the body’s immune system mistakes its own healthy tissues as foreign and attacks them. Autoimmune diseases are the third most common category of disease in the U.S. after cancer and heart disease and include over 80 disorders.

Common Autoimmune Conditions

Among the most common autoimmune disorders are:

  • Rheumatoid arthritis: the immune system targets the joints causing inflammation and pain.
  • Multiple sclerosis: characterized by the immune system attacking the protective covering of nerves, leading to communication issues between the brain and the rest of the body.
  • Lupus: can affect various organs such as the skin, joints, kidneys, and brain due to immune system dysfunction.
  • Type 1 diabetes: the immune system attacks insulin-producing cells in the pancreas
  • Celiac disease: the immune system reacts to gluten, damaging the lining of the small intestine.

These conditions vary widely in their symptoms and severity, but all share the common feature of the immune system turning against the body’s own tissues.

Consequences of Autoimmune Disease

Most autoimmune diseases cause inflammation, although the particular disorder will determine the symptoms and parts of the body that are affected. The common feature of any autoimmune disease is the immune system upregulating to the point where it starts attacking healthy cells in the body, thus causing tissue damage and inflammation.

Common symptoms, which may come and go and change in severity, include:

  • aches
  • pains
  • swelling
  • digestive disturbances
  • skin issues
  • fatigue

If you are suffering from these symptoms, contact your healthcare provider to learn how to get tested for autoimmune diseases.

Pathological Features

Autoimmune may best be described as a “mosaic disease,” a term first coined in 1989 by immunologist Yehuda Shoenfield. This is because the disease is often like a mosaic, with similar starting causes rearranged in different patterns, meaning that there are common factors that feed the disease but it will manifest differently depending on the individual.

There is a female predominance, meaning women have a higher incidence and prevalence of autoimmune diseases than men, and 85% or more patients of multiple autoimmune diseases are female.

Another feature is poly-autoimmunity. It is common for a person to have more than one autoimmune disease in their lifetime. Other than that, there seem to be three key factors that contribute to the development of autoimmune diseases:

  1. Genetic predisposition
  2. Environmental exposure
  3. Imbalance in immune regulation (when there’s more “killers” than “peacekeepers” in the immune system, in a healthy person with a regulated immune system this ratio is 50-50.

This can happen due to exposure to toxic chemicals, poor microbiome health or the new presence of microorganisms — live bacteria can breach body barriers into tissues and organs, upregulating a pro-inflammatory state of the immune system, causing “danger signals.”

Tissue state is very important in regulating autoimmunity, and necrotically dying calls are a signal of danger to the immune system, leading to a cycle in this sequence:

  1. tissue damage
  2. upregulation of immune reaction
  3. immune misdirection (attacks self)
  4. more tissue damage
  5. more immune upregulation
  6. more attacks on self, and repeat

Stealth Pathogens

These microorganisms that migrate into tissues and organs are known as “stealth pathogens” and can be in these places:

  • mouth
  • stomach
  • blood
  • lungs
  • bladder
  • brain
  • gut.

More than one type of pathogen can trigger autoimmune disease; however, particular microbes are associated with certain disorders. For example, a key pathogen in triggering the autoimmune disease Rheumatoid Arthritis is the Epstein Barr virus, and another is Proteus Mirabilis, a pathogen that causes urinary tract infections. In fact, there is a correlation between UTI infections and Rheumatoid Arthritis, and studies have confirmed that 90 days of cranberry juice decreased disease activity in women with this autoimmune disorder.

But this process involves much more than just a virus or bacterial infection like a UTI. There are multiple factors at play, and to become autoimmune, one also needs at least 2 or more “hits” of the following:

  1. Self and non-self similarity: pathogens often produce proteins that mimic host proteins, getting confused as “self” and thus going undetected
  2. Danger signals: defense reaction of immune system to dying/damaged tissue
  3. Self reactive T cells in tissue
  4. Person has a specific human leukocyte antigen (HLA) allele (genetic predisposition)
  5. Mechanisms that regulate the immune response are not fully functional

Gut Health

Another very important contributing factor to autoimmune diseases is poor gut health. When there is a loss of beneficial microbes, reduced microbiome diversity leads to a reduced function of the gut barrier, making it easier for opportunistic/pathogenic microbes to overgrow and breach the gut barrier — a condition known as “leaky gut.”

When this happens, our immune system gets involved due to the higher pathogen load, and can become hyper vigilant and over-stimulated when dealing with repeated and chronic immune challenges (one of the factors that leads to autoimmune).

Thus it is very important to have a healthy microbiome with good microbe diversity and a healthy gut lining to protect from barrier breaches. Prebiotics (from fiber) are especially important because they make short chain fatty acids like butyrate which bind to immune cells interleukin 10 and have a protective and anti-inflammatory effect.

Gut barrier disruptors that damage our gut barrier include:

  • Poor diet
  • Antibiotics and other drugs
  • NSAIDs
  • Gut dysbiosis
  • Stress
  • Disruptors (ie. gluten, pesticides, toxins)
  • Inflammation

Targeted Interventions

When it comes to managing autoimmune diseases, targeted interventions in the form of key strategies and herbs, a tailored autoimmune diet, and carefully selected supplements can work synergistically to support the body’s natural defenses and promote overall well-being.

Key Strategies and Herbs

Key strategies and herbs for autoimmune management include the following:

  1. Eliminate stealth pathogens if present – licorice, thuja, St John’s Wort, eleuthero and cat’s claw for viruses; myrrh, berberine, garlic, sage and cat’s claw for bacteria
  2. Eliminate gut dysbiosis – “Weed” – berberine, andrographis, oregano oil, anise oil, and “Feed” – prebiotic fiber, probiotics (at least 2 hours apart from “weed” herbs, or can be done on different days)
  3. Heal gut barrier – DGL, meadowsweet, chamomile, slippery elm and marshmallow
  4. Support immunity and immune modulation – echinacea, astragalus, medicinal mushrooms, rehmannia, hemidesmus, bupleurum, feverfew
  5. Support adrenals and HPA axis – Licorice and rehmannia, adaptogens
  6. Resolve chronic inflammation/reduce danger signals – essential to resolve inflammation, clear dead cells so tissue can heal – curcumin, boswellia, ginger
  7. Detoxification – Nrf2 detox pathways/reduce oxidative stress – turmeric, green tea, rosemary, grape seed, garlic, gotu kola, milk thistle

Protocol is usually done initially for 3 months, then 1 month per year as maintenance for stealth pathogens and gut dysbiosis. Herbs for inflammation and immune support/modulation may be taken for long term management. If you are on prescription medications check for any potential interactions with your health care practitioner or pharmacist.

Autoimmune Diet

Autoimmune diet can help with symptoms and management:

  • No gluten
  • No/minimal sugar
  • No dairy
  • No fried food
  • No yeast
  • No alcohol
  • Plenty of fiber (ie. psyllium, oat bran, gum arabic, butyrate)
  • Consider temporarily eliminating lectins (nightshade veggies and legumes) if antibody levels are high


If you’re looking to support your gut health as part of your autoimmune management plan, consider trying Gut Health Formula by Codeage or Gut Health by Trace Minerals Research.

Gut Health Formula by Codeage is a comprehensive supplement that includes a blend of prebiotics, probiotics, and digestive enzymes to support optimal gut function and promote a healthy gut microbiome.

Gut Health by Trace Minerals Research, on the other hand, focuses on providing essential trace minerals that are crucial for maintaining a healthy gut lining and supporting overall digestive health. Both supplements can be valuable additions to your autoimmune regimen, helping to promote a balanced and resilient gut environment.


Autoimmune diseases are complex disorders that arise from a combination of genetic predisposition, environmental factors, and imbalances in immune regulation. These “mosaic diseases” predominantly affect women and can manifest in various ways, causing symptoms such as aches, pains, swelling, digestive issues, skin problems, and fatigue. If you suspect you may have an autoimmune disease, it’s crucial to learn how to get tested for autoimmune diseases by contacting your healthcare provider.

To manage autoimmune diseases, a multi-faceted approach is essential. This includes addressing stealth pathogens, improving gut health, supporting the immune system, reducing inflammation, and promoting detoxification. An autoimmune diet that eliminates potential triggers and includes plenty of fiber can be beneficial. Additionally, incorporating specific herbs and supplements targeting various aspects of autoimmune disorders can help with symptom management and overall health improvement.



  • Webinar: Autoimmunity: the Immune Puzzle by Dr Kerry Bone for MediHerb
  • Book: Bone, Kerry. Functional Herbal Therapy: A Modern Paradigm for Clinicians. 2021 Aeon Books Ltd, London.
  • Journal: Desai MK, Brinton RD. Autoimmune Disease in Women: Endocrine Transition and Risk Across the Lifespan. Front Endocrinol (Lausanne). 2019 Apr 29;10:265. doi: 10.3389/fendo.2019.00265. PMID: 31110493; PMCID: PMC6501433.
  • Journal: Thimóteo NSB, Iryioda TMV, Alfieri DF, Rego BEF, Scavuzzi BM, Fatel E, Lozovoy MAB, Simão ANC, Dichi I. Cranberry juice decreases disease activity in women with rheumatoid arthritis. Nutrition. 2019 Apr;60:112-117. doi: 10.1016/j.nut.2018.10.010. Epub 2018 Oct 10. PMID: 30553231.