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What Is Autoimmune Disease, And How To Treat And Prevent It?

The incidence of autoimmune disease has skyrocketed over the past 50 years.

Today, a shocking one in five Americans suffers from an autoimmune disease – conditions that include disorders as varied as alopecia, psoriasis, hashimoto’s disease, rheumatoid arthritis, celiac disease, multiple sclerosis, lupus, and more – and this number is only expected to rise. (1) While conventional medicine has limited options for the treatment of autoimmunity, Functional Medicine offers an approach that can prevent and even reverse the course of these devastating illnesses.

Read on to learn about common autoimmune diseases, their underlying causes, and how to prevent and reverse autoimmune disease through strategic dietary and lifestyle changes.

What Is Autoimmune Disease?

Autoimmune disease occurs when the body’s normal immune defenses go awry and rather than attacking pathogens, begin attacking the body itself. (2) Autoimmunity is characterized by four overarching components: (3)

  1. An imbalance between effector T cells, which defend the body by producing an immune response, and regulatory T cells, which suppress the immune response
  2. Defective elimination or control of self-reactive immune cells, which are capable of attacking the body
  3. A chronically alert immune system
  4. Widespread inflammation

More than 80 different autoimmune diseases are currently known and some are well recognized, such as type 1 diabetes and multiple sclerosis, others are rare and difficult to diagnose. (4) Autoimmune disease disproportionately affects women. This phenomenon may be tied to the suppressive effect of testosterone, which is of course much higher in men, or the production of B cells, immune cells that can become self-reactive and trigger an autoimmune reaction. (5)

How Conventional Medicine Usually Treats Autoimmune Disease—and Why You Should Consider the Functional Medicine Approach

The conventional treatment approach for autoimmune disease relies heavily on pharmaceutical drugs. While these drugs are effective at suppressing symptoms, they can also have significant side effects.

Corticosteroids such as prednisone, methylprednisolone, and dexamethasone are used to reduce inflammation in those with autoimmune disease. However, long-term corticosteroid use can increase the risk for type 2 diabetes and may lead to weight gain, increased vulnerability to infections, and osteoporosis.

Immunosuppressants, including methotrexate and cyclophosphamide, stifle the body’s immune response. These drugs are associated with liver toxicity and can increase the risk of infections, as well as leukemia.

Biologic response modifiers, including etanercept (trade name Enbrel) and Infliximab (trade name Remicade), are used to modify the immune response. While often hailed as the “next frontier” in the medical treatment of autoimmune disease, they can have dangerous side effects, including central nervous system damage, cardiac reactions, severe allergic reactions, serious infection, and lupus-like syndrome. (6) While some people initially feel relief with the use of these drugs, loss of response to treatment is common. (7)

Clearly, the conventional treatment approach to autoimmune disease leaves much to be desired. It fails to address the underlying causes of autoimmunity, and the reliance on pharmaceuticals with so many possible side effects can harm the body over the long term. Functional Medicine, on the other hand, offers a viable alternative to potentially dangerous drugs. Rather than suppressing symptoms, Functional Medicine addresses the underlying causes of autoimmunity, relieving symptoms and even reversing the course of disease.

Autoimmunity: Genetics Load The Gun, But Your Environment Pulls The Trigger

Autoimmune diseases arise from a combination of genetic and environmental factors. Think of genetics as the bullet that loads the gun and environment as finger that pulls the trigger. Specific variations in genes, referred to in the scientific literature as polymorphisms, set the stage for autoimmunity by altering the regulation of immune cells. Environmental factors interact with these genes, pulling the trigger and activating autoimmunity. Research has identified a handful of genetic polymorphisms and environmental factors that trigger the autoimmune disease process.  

Genetic Factors That Influence Autoimmunity

Human leukocyte antigen (HLA) polymorphisms are the best-understood genetic risk factors for autoimmune diseases. (8) The HLA system plays a crucial role in the presentation of antigens (toxins or other foreign substances) to the immune system. Polymorphisms in HLA genes may impair the immune response to antigens, thereby impairing autoimmunity. HLA-DQ2 and HLA-DQ8 are well known for their role in celiac disease. HLA-DRB1 is linked to rheumatoid arthritis, and HLA-B27 to spondyloarthritis. Variations in cytokine genes may also increase the risk of autoimmune disease by producing excessive amounts of pro-inflammatory molecules. (9)

It is crucial to make the distinction that these genes increase the risk of autoimmunity but do not guarantee it will occur. Environmental triggers, discussed next, are the critical triggering factors that ultimately set off the autoimmune cascade.

Environmental Triggers for Autoimmune Disease

Gut Dysbiosis and Intestinal Permeability

Mounting evidence indicates that the gut microbiota significantly influences autoimmune disease risk. There are three primary mechanisms through which gut microbes impact autoimmunity:

  1. Gut microbes regulate T cell differentiation. In a healthy gut, bacteria regulate the differentiation of effector and regulatory T cells. Bacterial infection, on the other hand, induces apoptosis (cell death) of intestinal epithelial cells, which ultimately allows for the production of self-reactive T cells. (10, 11)
  2. Microbial enzymes modify proteins. Intestinal dysbiosis impacts the types of microbial enzymes present in the gut. Changes in these enzymes modify host proteins and may initiate an autoimmune response. (12)
  3. Leaky gut allows undesirable bacteria to travel. Increased intestinal permeability (aka “leaky gut”) is a “danger signal” that triggers the autoimmune disease process. (13) Leaky gut allows normally harmless bacteria to escape from the intestine into the systemic circulation, triggering an autoimmune attack. (14)

C-Section Birth

Infants born via C-section likely will have a gut microbiota colonized by abnormal bacteria, including Staphylococcus from the skin of their mothers, doctors, and other persons attending the birth, as well as pathogens found in hospitals. Conversely, infants delivered vaginally are colonized by their mother’s vaginal bacteria, which include beneficial Lactobacilli. Research indicates that the abnormal gut microbiota composition of C-section babies alters their immune system development and may increase their future risk of asthma, allergies, as well as autoimmune conditions. (15, 16)

Environmental Toxins

Environmental toxins are significant risk factors in the development of autoimmune disease. Mercury, a heavy metal present in certain types of seafood and dental amalgam fillings, initiates autoimmunity by altering the expression of immune system genes. (17)

BPA, the notorious plasticizer found in cash register receipts and plastic food storage containers, provokes autoimmunity by altering estrogen signaling, disrupting cytochrome P450 detoxification pathways, increasing circulating lipopolysaccharide, and activating macrophages. (why PLEIJ does not provide provide printed sales receipts… you’re welcome!) (18)

Phthalates, another common group of plasticizers, initiate thyroid autoimmunity by increasing oxidative stress. (19)

Last but not least, organic solvents, found in dry cleaning chemicals, paint thinner, standard nail polish removers, and detergents, increase the risk of autoimmune disease by inciting an inflammatory response and tissue injury. (20)

Excessive Hygiene

Microbial exposure in early life trains the immune system to distinguish between self and non-self. The immune system cannot develop normally in the absence of microbial inputs—i.e., dirt and germs. Our society’s obsession with disinfecting, scrubbing, and vacuuming away every speck of dust in our environment deprives our children’s developing immune systems of these microbial “teaching opportunities,” increasing their risk of immune dysfunction in the future. (21)


Celiac disease is the most well-understood autoimmune disease triggered by gluten. However, gluten also provokes non-celiac autoimmune disorders, including Hashimoto’s disease and Sjögren’s syndrome, by activating inflammatory pathways, altering the composition of the gut microbiota, and increasing intestinal permeability. (22)


Though a lack of microbial exposure contributes to autoimmune disease development, chronic infections with harmful pathogens also play a crucial role. Lyme disease provokes autoimmunity in the cardiovascular system and joints due to molecular mimicry between Borrelia burgdorferi and self-components naturally present in the immune system. (23, 24) H. pylori infection initiates thyroid autoimmunity, and cytomegalovirus exacerbates autoimmune neuroinflammation. (25, 26) For many people, treating pre-existing infection is a crucial part of the autoimmune disease healing process.

Mitochondrial Dysfunction

Mitochondrial dysfunction contributes to the development and progression of several autoimmune diseases, including multiple sclerosis (MS) and lupus. (27, 28) In addition to serving as the energy factories of our cells, mitochondria also regulate autophagy, the process by which cells “clean house” and break down unnecessary or dysfunctional components. Mitochondrial dysfunction leads to defects in autophagy, impairing the destruction of rogue self-reactive immune cells and potentially triggering autoimmune disease.

Chronic Stress

Psychological stress is an established risk factor for autoimmune disease. (29) Stress may trigger autoimmunity by altering the gut microbiota and by dysregulating the HPA axis, the body’s primary stress-response system that also influences immune function. (30)

Circadian Disruption

The activities of your immune cells are affected by your circadian rhythm, a set of biological processes that shape your behavior and physiology and follow a roughly 24-hour cycle. Factors that disrupt circadian rhythm may contribute to immune dysfunction. For example, research has shown that shift work, a significant circadian disruptor, is associated with autoimmune hypothyroidism and rheumatoid arthritis. (31, 32) Circadian disruption may also contribute to autoimmune diseases of the central nervous system, such as multiple sclerosis. (33)

Sleep Deprivation

Closely linked to circadian disruption, sleep deprivation increases the risk of autoimmunity. Chronic insomnia and sleep apnea are both associated with significantly increased risks of autoimmune disease. (34, 35)

While you can’t change the genetic cards you’ve been dealt, you can reduce your (and your children’s) risk of autoimmune disease by minimizing exposure to environmental factors that “light the fuel” of autoimmunity.

Minimize Antibiotic Use

There’s no question that antibiotics are vastly overused in our society. Excessive antibiotic use might contribute to autoimmunity by depriving the body of microbial exposures necessary for shaping immunity and by altering the gut microbiota. Unfortunately, research indicates that physicians continue to prescribe antibiotics for avoidable cases, so to minimize antibiotic use, you’ll need to be your own best advocate. (36) Limit antibiotic use only to situations in which it is absolutely necessary, keeping in mind that antibiotics are useless for viral infections, such as the flu, as well as for many colds and upper respiratory infections.

Increase Early Bacterial Exposure

While a hyper-hygienic environment during infancy and childhood may promote future autoimmune disease, greater microbial exposure early in life may significantly reduce this risk. Say no to hand sanitizer and antibacterial soap. These products contain chemicals that disrupt the skin and gut microbiotas and may alter immune system development in children. Here are some other tips to increase early bacterial exposure:

  • Use “green” cleaning products at home. Switch out harsh cleaners laden with synthetic antimicrobial agents for natural enzyme- and essential oil-based cleaning products; synthetic cleaning agents, such as triclosan, disrupt the gut microbiota and may impair the body’s immune response. (37) Triclosan also induces mitochondrial dysfunction, another contributing factor in autoimmune disease. (38)
  • Spend more time outdoors. Spending time in nature exposes the body to a variety of microbes, helping to form a robust immune system. (39)
  • Consider hand-washing your dishes, rather than machine washing. This surprising recommendation is based on research showing that children raised in households where dishes are hand-washed have a reduced risk of allergies compared to those raised in homes with automatic dishwashers. (40) Allergic diseases and autoimmunity follow a similar developmental trajectory, so the benefits of hand-washing dishes may extend to protection against autoimmune disease. (And while it’s not the right choice for every household, sharing your home with a dog is also associated with lower levels of allergies in kids, if they’re exposed to the animal as babies.) (41)

Importantly, it seems that increased microbial exposure must occur consistently in order to shape the development of a healthy immune system in childhood. Children living in hyper-hygienic conditions who experience only occasional exposure to farm animals actually see a worsening of inflammatory and allergic conditions in such an environment, presumably because their immune systems are unable to handle the sudden load of microbes and microbial byproducts. (42)

Increased microbial exposure in adulthood does not confer the same degree of immunoprotection as it does during childhood. However, following the recommendations outlined here will help you maintain a healthier gut microbiota, which plays a crucial role in protection against autoimmunity.

Avoid the Standard American Diet

The Standard American Diet of processed foods promotes autoimmune disease by impairing metabolic and immunologic mechanisms. (43) In addition to avoiding processed foods, identifying and eliminating foods that trigger inflammation, such as gluten, may also help prevent autoimmune disease. (44)

Eliminate Toxins

Avoiding environmental toxins is crucial for reducing the risk of autoimmunity. Tap water is laden with environmental contaminants, so we recommend investing in a high-quality water filter for your drinking and bathing water. Instead of aluminum or Teflon cookware, which leach heavy metals and toxic chemicals into food, use cast iron, enameled cast iron, or stainless-steel cookware. Finally, make sure your home isn’t a source of mold or mycotoxins; these contaminants significantly impair immune function and may promote autoimmunity. You can read more about the dangers of mold exposure in my article “5 Things You Should Know about Toxic Mold Illness.”

Try Breastfeeding

Research indicates that breastfeeding has powerful protective effects against the development of autoimmune disease in children. By introducing immune cells from mom into baby, breast milk shapes the development of the infant immune system and induces immunogenic tolerance, critical factors that may reduce future risk of autoimmune disease. (45)

Interestingly, the combination of breastfeeding and daycare attendance is associated with reduced risk of type 1 diabetes, whereas daycare without breastfeeding is linked to an increased risk of the condition. (46) This finding suggests that breastfeeding and exposure to environmental microbes (discussed next) work synergistically to modulate the developing immune system, whereas microbial exposure without concomitant breastfeeding may overwhelm the immune system.

Taking these steps could help you prevent autoimmunity from taking hold (and if you’re a parent, protect your child, as well), but what if you already have an autoimmune condition? Is it possible to cure autoimmune disease?

The First Step to Treating Autoimmune Disease: Diet

You can heal yourself from an autoimmune disease. The first step is to eat a diet devoid of inflammatory, gut-damaging foods, such as gluten. Research indicates that a gluten-free diet can halt the celiac disease process and alleviate symptoms of non-celiac autoimmune diseases. (47) However, gluten elimination may not be enough for many people. Consider trying one of the diets outlined below for a more comprehensive approach to treating autoimmune disease.


Making the transition from a Standard American Diet to a Paleo diet can produce dramatic improvements in autoimmune disease symptoms. Autoimmune diseases are rare (or nonexistent) in hunter–gatherer societies, so eating a diet that emulates that of hunter–gatherers may have benefits for inflammation and immunity. (48) Focus on eating organic vegetables and fruits, meat and poultry, organ meats, wild-caught seafood, starchy tubers, nuts and seeds, and healthy fats.

Autoimmune Protocol (AIP)

If Paleo is not enough, you may want to try the autoimmune protocol (AIP). This stricter version of Paleo is designed to remove all potentially inflammatory foods and has been found useful for alleviating symptoms of IBD. (49) In addition to eliminating grains, legumes, dairy, and industrial seed oils like standard Paleo, it eliminates eggs, nightshades, nuts and seeds, and seed-based spices. It includes non-nightshade vegetables, fruit, starchy plants such as sweet potatoes and cassava, meat and poultry, seafood, coconut products, and healthy fats. Due to the strict nature of AIP, it is intended to be followed only for a limited period, not forever.

Low-Lectin Diet

The low-lectin diet, developed by Dr. Steven Gundry, is based on the idea that lectins, a type of protein, play a significant role in autoimmune disease by increasing intestinal permeability and that limiting their consumption can reverse autoimmunity. (50) Lectin-rich foods include grains, legumes, potatoes, tomatoes, and squash.

Lectin sensitivity varies from one person to another. If you want to determine whether lectins are problematic for you, do some self-experimentation; for example, you may find that you tolerate squash and tomatoes just fine but need to avoid all grains and legumes.

Wahls Protocol

The Wahls Protocol is a Paleo-style diet that was developed by Dr. Terry Wahls of the University of Iowa. The diet, developed during her own battle with severe MS, is designed to supply all the nutrients required for healthy mitochondrial function. The protocol features nine cups of fruits and vegetables daily and emphasizes grass-fed meat, nutrient-dense organ meats, and bone broth. When combined with exercise, electrical muscle stimulation therapy, and stress-management techniques, the diet has been found to reduce fatigue and improve the quality of life, mood, and cognition in people with MS. (51, 52) You can learn more about the Wahls Protocol in my interview with Dr. Wahls.

Low-Starch Diet

As I mentioned earlier, HLA genetic variants contribute to autoimmune disease by altering immune function. People with a specific HLA variant called HLA-B27 have been found to have higher levels of an opportunistic pathogen called Klebsiella, whose growth is fueled by dietary starch. (53) Research suggests that individuals with the HLA-B27 variant and autoimmune disease may benefit from a low-starch diet that limits Klebsiella growth. Examples of low-starch diets include the specific carbohydrate diet (SCD) and the GAPS diet.

Ketogenic Diet

A very-low-carbohydrate, moderate protein, high-fat ketogenic diet has been found to improve mitochondrial function and decrease inflammation, thereby improving symptoms of autoimmune disease. (54) It appears most useful for autoimmune diseases of the central nervous system, such as multiple sclerosis. If you have autoimmune thyroid disease, you should probably steer clear, since the extremely low carbohydrate intake on the ketogenic diet can reduce thyroid hormone output.

Seven More Ways to Treat Autoimmune Disease Naturally

While conventional medicine offers few options beyond side-effect-laden drugs, for people with autoimmune disease, a Functional Medicine approach that incorporates ancestral health and lifestyle techniques can alleviate symptoms and potentially reverse the autoimmune process.

1. Heal Your Gut

Healing the gut is a crucial part of treating autoimmune disease. In addition to eating an anti-inflammatory diet, which promotes the growth of a healthy gut microbiota, probiotics may also be of use. In preclinical research, a probiotic called VSL #3 has been found to prevent autoimmune disease by modulating the gut microbiota and induce remission in IBD with efficacy equivalent to that of 5-ASAs, a standard class of drugs used in the conventional treatment of IBD. (55, 56) In human studies, probiotics alleviate the clinical severity of rheumatoid arthritis and improve symptoms and quality of life in MS. (57, 58)

2. Maximize Your Nutrient Intake

Ensuring an optimal intake of nutrients required by the immune system may also alleviate autoimmune disease symptoms. Vitamin A, found in liver and egg yolks, beneficially modulates the immune system and gut microbiota in autoimmune disease. (59) Vitamin D, obtained from sun exposure and fatty, cold-water fish, helps maintain the intestinal barrier by inducing the expression of tight junction proteins, thus protecting against leaky gut. (60) Zinc, found in meat and poultry, affects the maturation of effector and regulatory T cells, while selenium decreases TPO (thyroid peroxidase) antibodies in autoimmune thyroid disease patients. (61, 62) Finally, the omega-3 fatty acids EPA and DHA help maintain inflammatory balance in the body, while glutathione, the body’s master antioxidant, protects against autoimmunity by fine-tuning the innate immune response.

3. Consider Taking Low-Dose Naltrexone (LDN)

Low-dose naltrexone (LDN) is a medication used at very low doses for the treatment of autoimmune disease. It is an opiate antagonist and was originally developed for treating drug addiction, though at a much higher dosage. LDN has been found to reduce medication needs in rheumatoid arthritis, improve intestinal barrier function and inflammation in IBD, and inhibit the progression of MS. (63, 64) LDN is technically an off-label use of the drug naltrexone, so if you’re interested in this therapeutic option, you’ll need to get in touch with a prescribing physician familiar with its applications in autoimmune disease. You can learn more about LDN in my article “Low-Dose Naltrexone: A Promising Drug for Hard-to-Treat Conditions” and find a prescriber near you on the LDN Research Trust website.

4. Treat Infections

Pre-existing infections such as Lyme disease, H. pylori, and cytomegalovirus are overlooked but driving forces in the development of autoimmune disease. Treating these infections with a healthcare professional can help you make headway in your healing process.

5. Follow a Fasting Diet

The fasting mimicking diet (FMD) is an eating program designed to help people achieve the health-promoting effects of fasting while minimizing the adverse effects that are associated with prolonged calorie restriction. Research indicates that the FMD is beneficial in the treatment of autoimmune disease, promoting the regeneration of immune cells and reducing symptoms of autoimmunity. (65) You can learn more about the FMD in my blog “Rebooting the System: The Benefits of a Fasting Mimicking Diet.”

6. Minimize Your Stress

There are many ways to reduce stress: some people manage it by exercising, some engage in specific breathing exercises, while others prefer to engage in beloved hobbies such as reading and painting. While the stress-reduction techniques that work best for you will depend mainly on your personal preference, I believe everyone should consider incorporating meditation into their lives. Meditation has been scientifically proven to reduce stress, rewiring the brain to better handle whatever challenges life throws its way.

7. Correct Your Circadian Rhythm and Get More Sleep

Optimize your circadian rhythm by maintaining a consistent sleep/wake schedule, sleeping in a completely dark room, and avoiding blue light exposure at least an hour before bed to preserve melatonin production. Also consider time-restricted eating, a strategy in which food consumption is limited to a specific window of time each day, such as between 8 a.m. and 6 p.m.; research indicates that this practice syncs our circadian rhythms, leading to improved health. (66)

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