Triggers of Autoimmune Disease

 In Autoimmune/Allergy Medicine

Amanda Hegnauer, ND

Around 80 to 100 different autoimmune diseases have been identified, and at least 40 more diseases may have an autoimmune basis.1 The National Institutes of Health (NIH) estimates that roughly 23.5 million Americans suffer from autoimmunity, whereas the American Autoimmune Related Diseases Association’s estimate is more like 50 million.1 The difference is on account of the NIH number only including 24 diseases with good epidemiological studies behind them. According to the Department of Health and Human Services’ Office of Women’s Health, autoimmune-related disorders outranked all others in a list of the 10 most popular health topics among callers to the National Women’s Health Information Center.1An immune system disorder can be associated with either abnormally low activity or overactivity of the immune system. Immune deficiency diseases decrease the body’s ability to fight invaders, causing vulnerability to infections. In cases of overactivity, the body attacks and damages its own tissues. In response to an unknown trigger, the immune system may begin producing antibodies that attack the body’s own tissues instead of fighting infection. Common examples of autoimmune diseases include rheumatoid arthritis, systemic lupus erythematosus, and inflammatory bowel disease.

What triggers these diseases? At what point does the body decide that today is the day that antibodies flare and attack? Is it a specific trigger, or is it due to both physiological and/or psychological stressors built up over a period of time? Consider the foundation of naturopathic medicine that everyone is an individual. For some, perhaps, there is that 1 trigger; for others, disease results from layer upon layer of stressors that may culminate in the breakdown of the gut that leads to immune system activation and a flare. Common triggers include stress, genetics, and foods, especially those containing gluten or dairy, and the nightshade plant group. Additional concerns to consider include toxins and gut disorders.


Celiac disease is a classic example of an autoimmune disease involving a food trigger as well as a genetic component. In celiac disease, the body launches an immune response in the gut to a protein found in wheat gluten. Genetic variation in human leukocyte antigen (HLA) genes (on chromosome 6) predisposes to celiac disease; these genes are key regulators of the immune system.2 Scientists have detected several genetic variants that predispose a person to autoimmune disease. Some of these variants are within the genes that influence specific organs, whereas others are within the HLA cluster on chromosome 6 that affect the entire immune system. Psoriasis, for example, has been identified as having numerous clusters within the global immune system “control region” on chromosome 6. By distinguishing the relevant predisposition, treatment for autoimmune disease may then include the suppression of a specific amplifier.2


Foods that can damage the gut via an inflammatory reaction include dairy, gluten-containing grains, sugars, and the nightshades, among others. Casein, the main protein found in milk and other dairy products, can also trigger inflammation in many people. A safer alternative for some patients with autoimmune disorders are fermented dairy products such as grass-fed whole yogurt or kefir. Many people with autoimmune concerns already avoid gluten but still consume grains like corn, oats, and rice. Although this is a well-intended decision, these grains can also cause reactions in many individuals. Nightshade plant foods, including tomatoes, peppers, potatoes, eggplant, and some spices, contain alkaloids that are also capable of promoting an inflammatory response in some individuals.

Sugar, including agave and other organic forms, also affects the immune response. In one study,3 10 healthy people were assessed for fasting blood-glucose levels and the phagocytic index of neutrophils, which measures immune-cell ability to envelop and destroy invaders such as cancer. This small study revealed that by eating 100 grams (24 tsp) of carbohydrates from glucose, sucrose, honey, or orange juice, the capacity of neutrophils to engulf bacteria was significantly decreased; the neutrophils became “paralyzed.”3

Gut Concerns

In the past, I have referred to the gut as the center of our universe. Consider further evidence that supports this notion… The majority of the immune system resides in what’s referred to as the microbiome, the collection of microbes that reside in the human body.4 This is a sophisticated ecosystem consisting of trillions of bacterial colonies. Although these microbes are found within all parts of the body that are exposed to the environment (eg, mouth, skin, vagina), most of them reside in the gut where nutrients are in constant supply. The microbiome controls not only the immune system but also the brain, hormones, and genetic expression.

Pathology results when the microbiome is compromised. Increased permeability of the gut lining, aka “leaky gut,” predisposes to autoimmunity.5 A leaky gut can be caused by triggers such as a food sensitivity, an autoimmune condition (eg, antibodies attacking the gut lining), or medications that alter the gut lining, such as steroids. Small intestinal bacterial overgrowth, or SIBO, occurs when normal bacteria in the microbiome spread from the large intestine (where they belong) into the small intestine. This can also lead to a number of localized autoimmune conditions, such as post-infectious IBS6 and acid reflux.7 Chronic SIBO can also damage the gut, such that undigested food proteins and bacterial endotoxins can pass through the protective gut lining, thereby increasing the risk of an autoimmune reaction anywhere the body.8

Environmental Factors

Autoimmunity doesn’t usually produce clinical symptoms unless an additional event such as an environmental factor induces its expression.9 Many different environmental factors can affect the immune system in a way that triggers autoimmunity. Through molecular mimicry, for example, bacterial, parasitic, or viral infections can induce and exacerbate autoimmune diseases.9 Examples include the link between lupus and Epstein Barr virus infection, and the link between pediatric autoimmune neuropsychiatric disorders and streptococcal infection.9 Other triggers for autoimmune reactions include occupational and other chemical exposures.9


I know you have heard, “I never felt well since…” Folks know their bodies well enough to often pinpoint the precise date at which they started to decline. This is brilliant; however, what has occurred years prior? What led them to this exact date? As I have discussed previously, the etiology of autoimmune diseases is multifactorial; genetic, hormonal, environmental, and immunological factors can all play a role in their development.10 At the same time, the onset of at least half of all autoimmune disorders are thought to be due to “unknown trigger factors.”10

Stress – both physical and psychological – has been implicated in the pathogenesis of autoimmune disease.10 Many studies have also found that up to 80% of patients with autoimmune conditions reported unusually high emotional stress before the onset of their disease. Not only does stress promote disease, but disease can also causes profound stress in the patient, creating a vicious cycle.

Consider the possible role of psychological stress, and of stress-related hormones, in the development of autoimmune disease. The stress-triggered neuroendocrine hormones are thought to promote immune dysregulation, which eventually leads to autoimmunity by upregulating cytokine production.10 The treatment of autoimmune disease should therefore encompass stress management, including behavioral intervention, to help maintain immune balance.


Because triggers of autoimmune disease vary, treatment will also vary, based on the working diagnosis. Basic naturopathic philosophy serves as an ideal foundation for an individualized approach. Focusing on inflammation and gaps in the nutritional base is the perfect start for long-lasting results. Working closely with your patient as his or her symptoms ebb and flow is very important, as the chronic disease changes alongside your protocol. And remember that treating psychologically is just as important as treating physiologically.

Amanda Hegnauer, ND, Amanda Hegnauer, ND, is a licensed primary care naturopathic doctor in New Hampshire. She earned her doctorate from SCNM in Tempe, AZ. She is a member of the NH Association of Naturopathic Doctors (and in the past served as Executive Coordinator) and the Association for the Advancement of Restorative Medicine. Currently she sits on the State of NH Naturopathic Licensing Board. Dr Hegnauer practices at Hegnauer Holistic Health in Concord, NH, and at Cougar Sound Spirits Healing Center in North Sutton, NH. She also lectures within the community and acts as a Wellness Educator for the Concord CoOp. Particular interests include chronic fatigue, autoimmune diseases, endocrinology, gastroenterology, and women’s health (including menopause and bioidentical HRT).


  1. American Autoimmune Related Diseases Association, Inc. Autoimmune Statistics. AARDA Web site. Accessed October 1, 2015.
  2. GB HealthWatch. Autoimmune Diseases: Genes and Triggers. Available at: Accessed October 1, 2015.
  3. Sanchez A, Reeser JL, Lau HS, et al. Role of sugars in human neutrophilic phagocytosis. Am J Clin Nutr. 1973;26(11):1180-1184.
  4. American Microbiome Institute. Introduction to the Human Microbiome. 2015. Available at: Accessed October 1, 2015.
  5. Campbell AW. The Gut, Intestinal Permeability, and Autoimmunity. Alternative Therapies. 2015;21(1):6-7.
  6. Rodríguez LA, Ruigómez A. Increased risk of irritable bowel syndrome after bacterial gastroenteritis: cohort study. BMJ. 1999;318(7183):565-566.
  7. Kim KM, Kim BT, Lee DJ, et al. Erosive esophagitis may be related to small intestinal bacterial overgrowth. Scand J Gastroenterol. 2012;47(5):493-498.
  8. Lauritano EC, Valenza V, Sparano L, et al. Small intestinal bacterial overgrowth and intestinal permeability. Scand J Gastroenterol. 2010;45(9):1131-1132.
  9. Molina V, Shoenfeld Y. Infection, vaccines and other environmental triggers of autoimmunity. Autoimmunity. 2005;38(3):235-245.
  10. Stojanovich L, Marisavljevich D. Stress as a trigger of autoimmune disease. Autoimmune Rev. 2008;7(3):209-213.
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