Is Lyme Disease an Autoimmune Disease or is it the Trigger?

Lyme disease is an infection transmitted by a bite from an arthropod (insect or spider) vector, such as a deer tick. However, Lyme disease is often associated with autoimmunity, including positive antinuclear antibodies (ANA), rheumatoid factor (RF), and symptoms such as joint swelling and rashes. Autoimmune disease is a condition in which the immune system erroneously attacks and destroys cells and tissues in your body. While Lyme disease and autoimmune diseases have classically been considered distinct conditions, the lines between these two diseases are blurring as our scientific understanding of infection and the immune system evolves. 

The topic of Lyme disease and autoimmunity is complicated. Infectious disease experts disagree about whether Lyme disease triggers autoimmunity or whether previous Lyme infection can cause subsequent autoimmunity without an active infection. (1) Read on to learn more about the Lyme disease autoimmune connection and how nutrition can be used, alongside chronic infection treatment, to alleviate the autoimmune process and promote recovery. 

Is Lyme Disease Autoimmune?

The relationship between Lyme disease and autoimmunity is controversial. Some researchers in the Lyme disease space claim that chronic Lyme disease doesn’t exist. They argue that people previously infected with Lyme disease who experience symptoms beyond the standard course of antibiotics are suffering from a purely autoimmune phenomenon, referred to as “post-treatment Lyme disease” or a “post-Lyme autoimmune syndrome.” However, those who argue for the existence of post-Lyme autoimmune syndrome don’t ask, what might be the cause of the autoimmunity? The term “post-Lyme autoimmune syndrome” discredits the possibility of chronic, ongoing Lyme disease infection as an autoimmune trigger. So what is the truth? Can chronic Lyme disease cause autoimmunity?

Lyme disease is known to evade antibiotic treatment and persist in the body, creating a chronic infection. (2) As we’ll discuss shortly, there are several known mechanisms through which chronic infections trigger autoimmune processes. Based on the available research, it is highly likely that chronic Lyme disease triggers autoimmunity, NOT that autoimmune disease spontaneously appears after Lyme treatment, in the absence of ongoing infection. 

How does Lyme disease trigger an autoimmune response? Here are a few mechanisms linking Lyme disease and autoimmune disease: 

Lyme Infections Triggers IL-17, Which Triggers Autoimmunity

The Lyme disease autoimmune response appears to be mediated by an immune signaling molecule called IL-17. Early infection with Borrelia burgdorferi, the bacterium responsible for classic Lyme disease, triggers the production of interleukin-17 (IL-17), a pro-inflammatory cytokine that regulates the immune response. IL-17 is helpful in the early stages of infection for defending the body against infection. However, chronic Lyme disease may lead to excessive production of IL-17; at high levels, IL-17 can trigger autoimmunity. (3)

Lyme Disease Alters Immune Cell Communication

Recent research out of Johns Hopkins University indicates that Borrelia burgdorferi alters communication between two types of immune cells – dendritic cells and T-cells. (4) Dendritic cells are cells that process antigens, toxic or foreign substances that induce an immune response in the body. Examples of antigens include bacterial toxins and food proteins. After processing antigens, dendritic cells pass the antigens on to T-cells, which are specially “trained” cells that are able to target and destroy specific pathogens. Borrelia appears to interfere with the normal communication between dendritic cells and T-cells, causing the receptors on dendritic cells to change structurally and induce T-cells to attack healthy cells in your own body. 

Autoimmunity Through Molecular Mimicry 

Molecular mimicry is the process by which infectious or chemical agents induce autoimmunity due to similarities between the foreign substances and proteins in the body. When the immune system launches an attack against the foreign substances, the similarly-structured proteins can be caught in the crossfire, triggering an immune system attack against these self-substances. It is well established in the scientific literature that Borrelia burgdorferi can activate molecular mimicry, suggesting another mechanism through which it may cause autoimmunity. (5)

Lyme Biofilms May Trigger Autoimmunity

Research indicates that up to 80 percent of bacterial infections in humans are associated with biofilms (6), which are communities of microbial cells embedded in an extracellular (outside the cell) matrix that protects the bacteria from antibiotics. Borrelia species that cause Lyme disease are known to form biofilms, which help the bacteria evade antibiotic treatment. (7) Biofilms contain significant amounts of bacterial DNA, which can bind to a person’s own DNA and thereby trigger a self-attacking autoimmune response. 

Autoimmune diseases associated with Lyme disease include: 

  • Dermatomyositis (8, 9): Dermatomyositis is an inflammatory condition characterized by muscle weakness and a skin rash. It is widely thought to be an autoimmune disease. 

  • Guillain-Barre Syndrome (10): Guillain-Barre syndrome is a rare condition in which the immune system attacks the nerves, resulting in weakness, tingling, and paralysis. 

  • Sjogren’s Syndrome (11): Sjogren’s Syndrome is an autoimmune disease in which the immune system attacks the cells that produce saliva and tears. Sjogren’s syndrome often co-occurs with other autoimmune diseases such as rheumatoid arthritis and lupus. 

  • Systemic lupus erythematosus (SLE) (12): SLE, also known simply as “lupus,” is an autoimmune disease in which the immune system attacks tissues throughout the body, including the joints, skin, kidneys, and heart. 

The Lyme Disease and Lupus Connection

Numerous studies point to a connection between Lyme disease and lupus. Case studies of individuals with lupus and Lyme disease show high levels of lupus anticoagulant and positive ANA (antinuclear antibodies). (12

Lyme Disease & Hashimoto’s Disease 

Emerging research indicates that proteins from Borrelia burgdorferi may be capable of triggering autoimmune thyroid disease, causing autoimmune hypothyroidism. (13) This risk may be particularly relevant for people with specific genetic risk factors in their HLA-DR genes. The HLA DR genes are a family of genes that regulate the presentation of antigens to the immune system for the purposes of either stimulating or dampening an immune response. Molecular mimicry may be the mechanism connecting Lyme disease and Hashimoto’s disease. (14)

Other Tickborne Infections and Autoimmunity

Lyme disease is often not transmitted in isolation. The bite of a tick or another vector that transmits Lyme disease, such as biting flies, can transmit numerous other pathogens that can trigger autoimmunity. For example, Babesiosis, caused by the microscopic parasites Babesia microti and Babesia duncani, is also associated with autoimmunity, including positive ANA (antinuclear antibodies). (15

Can Antibiotic Treatment for Lyme Disease Initiate Autoimmunity?

Interestingly, some authors note that although Lyme infection itself may trigger autoimmunity, microbiome disruption resulting from antibiotic treatment for Lyme disease could also be an underlying mechanism linking Lyme disease to subsequent autoimmunity. (16) For example, antibiotic use is connected to a higher risk of rheumatoid arthritis, which attacks the joints. (17) It seems possible that antibiotic use could trigger autoimmunity based on its adverse effects on the gut microbiota, a critical regulator of immune function. 

How to Properly Manage Lyme Disease Autoimmunity

Clearing Lyme disease and other chronic infections is essential for resolving autoimmunity when a chronic infection is the root cause of autoimmunity. A Lyme-literate doctor can guide you through Lyme treatment. However, while you’re undergoing Lyme treatment, what can you do to resolve autoimmunity and improve your symptoms and health? Conventional medicine has a minimal repertoire of treatments for autoimmunity, namely broad-spectrum immunosuppressants that are toxic and can have widespread, long-term damaging effects. A functional medicine approach that includes strategic nutritional changes is a powerful and safer alternative to immunosuppressants for addressing autoimmunity during Lyme treatment. The autoimmune protocol (AIP) diet is particularly effective for autoimmunity. 

The Autoimmune Protocol (AIP) Diet

The AIP is a specialized version of a Paleo diet that eliminates foods that may stimulate the immune system and harm the gut, where much of the immune system resides and where autoimmunity is theorized to begin in many cases. (18) AIP also focuses heavily on optimizing dietary nutrient density and incorporating foods that mitigate inflammation and support a healthy gut. I (and countless other functional medicine providers) have used AIP innumerable times with clients to reduce and even reverse autoimmune disease processes with excellent results. In recent years, the autoimmune protocol has been studied in scientific trials and found to improve symptoms and markers of autoimmune activity in people with autoimmune diseases, ulcerative colitis, and Crohn’s diseases, including reducing calprotectin. (19, 20) The AIP diet has also been found to decrease systemic inflammation and improve symptoms and quality of life in Hashimoto’s disease. (21)

The AIP removes the following foods from the diet for at least three months:

  • Dairy

  • Grains

  • Legumes 

  • Nightshades, such as tomatoes and peppers

  • Nuts and seeds

  • Eggs

  • Seed-based spices 

  • Alcohol 

  • Coffee

The AIP diet emphasizes eating a wide variety of nutrient-dense, anti-inflammatory, gut-healing foods, including:

  • Red meat and poultry: Quality is essential here. Try to choose organic and grass-fed red meat and poultry or wild game.

  • Fish and shellfish: Emphasize wild-caught fish as much as possible.

  • Organ meats: Organ meats are a nutritional powerhouse, rich in nutrients that support the immune system, such as zinc and iron. 

  • Leafy greens

  • Cruciferous vegetables, such as arugula, broccoli, cauliflower, and kale

  • Allium vegetables, such as garlic, onions, and leeks

  • Root vegetables, such as carrots and parsnips

  • Winter squashes, such as acorn and butternut squash

  • Fruits, including berries, citrus fruits, avocado, and coconut

  • Herbs and spices

  • Healthy fats, such as olive oil, avocado oil, and coconut oil 

The AIP is a strict diet as it is not meant to be followed in its most rigid form over the long term. Instead, it is intended to be used over the short term to quell the autoimmune process while other underlying contributors to autoimmunity are being addressed. However, the diet itself may also help correct autoimmunity by supplying the foods and nutrients the body requires for well-regulated immune function and optimal gut health. Ultimately, specific foods are reintroduced into the diet over time to expand dietary diversity.  

The AIP diet is complex and is best undertaken under the guidance of a nutritionist, and it is crucial to ensure that nutritional needs are being met on the AIP diet. I routinely guide clients through the AIP diet in my private practice. If you’re interested in learning more about how you can work with me one-on-one in my nutrition practice, you can reach me here

Gut Healing and Stress Management Are Essential for Healing Lyme Autoimmunity 

Gut health significantly impacts immune system function, including the development and progression of autoimmunity. Healing your gut may improve Lyme disease-associated autoimmunity by balancing immune system function. When it comes to healing the gut, it’s essential to test, not guess, using a functional medicine stool test and SIBO testing. 

Stress management is also essential for healing Lyme disease and autoimmunity since chronic stress suppresses immune function and promotes autoimmune processes. A functional medicine provider can help you gauge your stress response with a test such as the DUTCH Adrenal profile. I often use this test in practice to see how my clients’ stress response is working and whether stress response support is needed. In addition, practices such as daily movement, meditation, and high-quality sleep are vital for managing stress and regulating the immune system in Lyme disease. 


Chronic Lyme disease can trigger autoimmunity through several mechanisms, including increased production of inflammatory signaling molecules like IL-17, altered immune cell communication, molecular mimicry, and biofilm formation. People who have previously been infected with Lyme disease and subsequently develop autoimmunity are more likely suffering from an ongoing infection that is disrupting immune function than spontaneous autoimmunity; “post-Lyme autoimmune syndrome” is thus an unhelpful construct that may cause people with autoimmunity triggered by infection to be improperly treated. It is crucial that nutrition, gut health, and stress be addressed to properly manage Lyme disease autoimmunity, alongside pharmaceutical treatments.

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