Autoimmune Disease

by | Aug 15, 2023 | Articles, Autoimmune, Conditions

Autoimmune disease is caused by the immune system attacking one’s own body, instead of doing it’s normal job of defending against foreign invaders such as bacteria, viruses, etc.  For example, in rheumatoid arthritis the target is joints, in type 1 diabetes the target is the pancreas, in Hashimoto’s thyroiditis the target is the thyroid, and so on.

How does autoimmune disease get started?

Normally the immune system is balanced between attack and tolerance.  That is, it remains quiet until an invader poses a threat, then it attacks.  And it tolerates a variety of non-threats, such as the hundreds of species of normal bacteria that live in harmony within us, the foods we eat, and the surrounding environment. Our immune system has a built in regulation system in the form of a certain immune cell called a T cell.  One type in particular is called “T regulatory” and I think of him as the air traffic controller for the immune system, telling other immune cells when and how to attack, or in this case telling rogue immune cells to stop their attack on the body.  The loss of this immune regulation is often part of autoimmune disease. In general, autoimmune disease starts due to a combination of processes. Sometimes it is one main issue, but most of the time it seems to be a collection of issues that finally tip the system out of tolerance and into attack mode.  Typically this is a combination of genetic susceptibility, dysbiosis, leaky gut, toxins, infections and/or immune reactive foods.

Genetic Susceptibility

Most people with autoimmune disease have a genetic predisposition for such.  Specifically they have a mutation in the part of their genome that codes for their “self recognition” markers.  Every cell in our body normally has a specific tattoo, so to speak, that is unique to each individual, and this is how our immune system tells friend from foe.  The tattoo is actually a protein marker called the “major histocompatibility complex”.  If a cell does not have this marker or has a different market then the immune system considers it a foe and attacks. We could now take a newborn baby and easily run the genetic test to examine these mutations and determine what autoimmune diseases that person will be susceptible to throughout their lifetime.  Note the key word here is susceptible.  The mutation does not at all guarantee the autoimmune process will start, and in fact estimates are that only 10-15% of people with these markers will go on to get the autoimmune disease.  In addition to genetics, they need a trigger, or multiple triggers to initiate the process.


There are over a 100 trillion bacteria that live in our intestinal tract – more than the 10 trillion cells in our body.  Humans have about 23 thousand genes, while the intestinal bacteria altogether harbor about 3 million genes. These bacteria are not parasitic passengers, but rather symbiotic participants in our overall health.  They depend on certain nutrients and behaviors that have been forged over thousands of years.  If we do right by them, they will support and modulate our immune system, defend against infections, help break down our food, generate essential vitamins, metabolize hormones and bile acids, supply the intestine with energy, and stimulate the normal motility of the intestine. Did you know the largest part of the immune system surrounds the gut?

The “gut associated lymphoid tissue” provides about 80% of the infection fighting white blood cells called lymphocytes.  This lymphocyte arsenal includes immune system controllers called T cells, antibody producing B cells, and stealth defenders called natural killer cells. The normal functioning gut “teaches” the immune system how to behave, starting at birth with the inoculation of bacteria during passage through the birth canal and furthered by breast-feeding.  During the first few years of life the ingestion of bacteria on food, dirt, and other normal things continue to instruct, balance and support the immune system.  Throughout life it is profoundly influenced by what is in the gut and what gets through the gut wall.  A normal, balanced immune system relies on a normal gut.

Dysbiosis is a microbial imbalance in which the normal healthy population of intestinal bacteria is disturbed, and it can be just as devastating to our health as any other unhealthy organ, perhaps in more subtle ways.  Unhealthy diet, antibiotics, chlorinated water, toxins, and more can cause dysbiosis.  The immediate result of dysbiosis may be nutrient deficiencies, toxin accumulation, bowel irregularities, inflammation, pathologic microbial infections, immune system imbalances, and as defined next, a leaky gut.

Leaky Gut

With a total surface area of about 500 square yards, the intestine forms the largest interface between our internal system and the outside world.  The gut lining is in constant contact with potential immune stimulators such as foodstuffs, toxins, microbes, parasites and allergens.  Every single substance that passes through the gut wall is carefully presented to the immune system and undergoes a thorough identification process. The lining of the intestine is covered with a biofilm of mucus and beneficial bacteria, much like a screen filter, providing a first line of defense against abnormal invaders.  Below this filter lie block-shaped cells that are bound together by tight junctions providing very specific regulation of what is allowed to pass between the cells.  Immediately below these cells is the circulation and the immune system.

The term “leaky gut” refers to damaged tight junctions that allow substances inside the gut to pass freely between the cells into the circulation where the immune system is then activated.  Many things, such as dysbiosis, infections, medications, toxins, nicotine, alcohol, stress and even foods, can cause leaky gut.  Certain beneficial bacteria protect and repair the tight junctions. In the case of leaky gut, the immune system is constantly activated and dumps inflammatory chemicals that wreak havoc throughout the body.  Symptoms such as fatigue, brain fog, anxiety, and depression are common with leaky gut.  Weight loss is nearly impossible if one has leaky gut due to disrupted hormone systems caused by the inflammation.  The immune system imbalances can lead to diseases associated with impaired defenses (e.g. bronchitis, sinusitis) or hypersensitive defenses (e.g. allergies, asthma, hives, autoimmune).


Various toxins can cause dysbiosis, leaky gut, or direct insult to the immune system.  These toxic chemicals are found practically everywhere in our surroundings, including building components, household cleaning products, pesticides/fungicides/herbicides in our food, chemicals in our water, and even in personal health and beauty products.  Heavy metals such as lead, arsenic, cadmium are a problem as well.  For many people a toxic exposure of some sort is the final trigger before their autoimmune disease begins.

Molecular Mimicry

At this point we need to define molecular mimicry.  This is a process in which our immune system recognizes a foreign invader, be that an organism, a food or even certain chemicals, and makes specific antibodies to target that invader.  Back to genetic susceptibility, due to mutations in self recognition markers, certain body tissues may look similar to the invader and the immune system will also attack the body.  Now we have autoimmune disease.  Sometimes eliminating the invader will stop the autoimmune mimicry, but other times the autoimmune process still continues as it still “sees” the invader in the form of self tissue.

Immune reactive foods

Most of us have varying degrees of health problems caused by the immune reactive foods we eat.  Foods that stimulate an abnormal immune reaction can lead to many common symptoms and diseases, and surprisingly many foods we think of as healthy are culprits.  Moreover, these foods are often ones we frequently eat.

The main antibody in this immune reaction is called IgG and it can be tested in a blood sample.  These immune reactions do not happen immediately, as they do with food allergies involving the immediate hypersensitivity pathway and histamine.  IgG immune reactions to foods takes 12-72 hours to get going.  And they can be sneaky without obvious connections to symptoms.  Eating a certain food even just a few times per week can generate significant immune activation, inflammation, and symptoms.  The connection to autoimmune can be through general immune system overload or through molecular mimicry.  Sometimes patients get lucky and simply eliminating a certain food will put their autoimmune disease into remission.


Infections may be the single most important trigger for developing autoimmune disease.  In this case it is due to molecular mimicry.  Even after the pathogen is eliminated the immune system may carry on the attack against self.  In these cases we typically proceed with low dose immunotherapy as a means to turn off the hyperactive immune attack.  With each autoimmune disease there is varying amounts of research into this infection trigger and that tends to guide our immunotherapy choices.  Other times there is little research and clinical history guides us.  For example, in someone who had frequent strep throat as a kid we might try the strep antigen mix.  Or someone who had a “flu” like illness just before their autoimmune disease presented, we might use various viral antigen mixes such as cold viruses or the Epstein-Barr virus mix.  Checking for antibodies to infectious agents is another way to guide us to choosing which antigen mix to choose.

Treatment Protocol

As with most any health issue we start with cleaning up the diet, managing stress, getting restful sleep and regular exercise.  These are all critical components for a proper functioning immune system, and good health in general.  A simple detox and shift to a low inflammatory autoimmune paleo diet works for some.  We usually test for immune reactive foods, and sometimes test for leaky gut.  We may order a comprehensive digestive stool analysis to analyze the microbiome, digestion and inflammation in the gut.  We may also order urine tests for toxic chemicals, heavy metals, or mold toxins.  Remove as much toxin exposure as possible from your diet and environment.  Remove heavy metals with some form of chelation.  Sometimes we use natural supplements to shift the balance of the immune system or peptide therapies such as Thymosin alpha-1 or beta-4.  Finally, low dose immunotherapy is often the “magic bullet” that turns off the autoimmune process.

Author Scott Rollins, MD, is Board Certified with the American Board of Family Practice and the American Board of Anti-Aging and Regenerative Medicine.  He specializes in bioidentical hormone replacement for men and women, thyroid and adrenal disorders, fibromyalgia and other complex medical conditions.  He is founder and medical director of the Integrative Medicine Center of Western Colorado ( and Bellezza Laser Aesthetics (   Call (970) 245-6911 for an appointment or more information.

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