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A Functional Medicine Chronic Lyme Disease Protocol

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A Functional Medicine Chronic Lyme Disease Protocol

Lyme disease, a tick-borne illness caused by the bacterium Borrelia burgdorferi, affects approximately 470,000 people in the United States annually. While most people recover from Lyme disease with appropriate antibiotic treatment, about 10% of individuals continue to experience lingering symptoms even after treatment, a condition referred to as Chronic Lyme Disease or Post-Treatment Lyme Disease Syndrome. These persistent symptoms can significantly impact a person's quality of life, making it vital to explore alternative approaches to manage and treat the condition. Functional medicine offers a comprehensive and holistic approach to addressing chronic Lyme disease by identifying and addressing the root causes of the illness.


What is Chronic Lyme Disease?

Lyme disease is an infection resulting from the Borrelia burgdorferi bacterium. In most instances, oral antibiotics effectively treat the condition. However, for some patients, fatigue, pain, and joint and muscle aches persist even after treatment. The term "chronic Lyme disease" has been utilized to describe individuals with various illnesses. While it is occasionally used to refer to patients with Lyme disease, it has also been applied to describe symptoms in people who show no clinical or diagnostic evidence of current or previous infection with B. burgdorferi. Due to the ambiguity surrounding the term chronic Lyme disease and the absence of a well-defined clinical definition, many experts in this area do not endorse its usage and instead refer to the disease as Post Treatment Lyme Disease Syndrome (PTLDS).

Chronic Lyme Disease Symptoms

Common symptoms of chronic Lyme disease include (5,6,7,8):

  • Persistent fatigue
  • Cognitive difficulties (brain fog, memory problems)
  • Neuropathy (tingling, numbness, or burning sensation in the extremities)
  • Sleep disturbances
  • Sensitivity to light and sound
  • Musculoskeletal pain
  • Arthritis and joint pain

What Causes Chronic Lyme Disease?

Chronic Lyme disease is controversial in the medical field and arises from several potential factors. Some experts argue that it results from an ongoing infection with the Borrelia burgdorferi bacterium, while others believe it is a collection of symptoms with no definitive underlying cause. Research is still ongoing to understand the exact cause, but certain factors have been proposed. Persistent infection is one such factor, with some studies indicating that the bacterium may continue to exist in the body even after antibiotic treatment, leading to ongoing symptoms. Another potential factor is immune dysfunction, where the immune system continues to attack the body even after the infection has been treated, causing inflammation and persistent symptoms as well as a weakened immune system due to unregulated inflammation. Moreover, several clinical factors surrounding the initial onset of Lyme disease have been found to increase the risk of persistent symptoms after treatment. These factors include the severity of the disease at onset, pre-existing conditions, and delays in diagnosis and proper treatment. Lifestyle factors such as poor diet, lack of exercise, and high-stress levels can contribute to a weakened immune system, making it more challenging for the body to recover from the disease.

Functional Medicine Labs to Test for Root Cause of Chronic Lyme Disease

To identify the root cause of Chronic Lyme Disease and develop an appropriate treatment plan, functional medicine practitioners may utilize the following tests:

Lyme Disease Testing

The Lyme Serology IgG/IgM test detects both IgG and IgM antibodies to B. burgdorferi in the blood. IgM antibodies are usually produced in the early stages of infection, while IgG antibodies appear later and can persist for months or years after the infection has resolved.

This test can help determine if a patient has been exposed to the bacterium and if the immune system has responded to it. If the test is positive or equivocal, a second test, such as the Lyme ImmunoBlot IgG + IgM should be performed as per CDC guidelines. This test is a more specific type of serological test known as a Western Blot or Immunoblot. It detects IgG and IgM antibodies to specific proteins of B. burgdorferi, providing a more detailed view of the immune response to the bacterium.

However, it is important to note that a positive serology doesn't always indicate an ongoing infection, and a negative one doesn't rule out the possibility of persistent symptoms. Studies underscore the significance of conducting tests such as complete blood count (CBC), metabolic panel (CMP), thyroid testing, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) during the initial evaluation of PTLDS to rule out other disorders. These disorders include severe anemia, liver or kidney issues, metabolic conditions like diabetes, as well as other inflammatory or autoimmune diseases.

Comprehensive Stool Testing

The Vibrant Wellness Gut Zoomer 3.0 Complete test is an advanced stool analysis that can offer valuable insights for individuals with chronic Lyme by evaluating the composition and health of the gut microbiome. As PTDLS has symptoms that overlap with conditions involving a dysbiotic microbiome, researchers have identified a distinct gut microbiome signature in patients with PTLDS that differs from that of healthy control subjects or intensive care unit (ICU) patients.

The Gut Zoomer 3.0 Complete test detects and quantifies various microorganisms in the gut, such as bacteria, fungi, parasites, and viruses. This test helps to identify potential overgrowth or deficiencies of specific microorganisms, including an increase in Blautia and a decrease in Bacteroides, which have been shown to potentially contribute to immune system dysfunction in PTLDS patients. Moreover, the test examines markers of inflammation, immune response, and digestive function, providing a better understanding of the underlying factors contributing to PTLDS symptoms.

Micronutrient Testing

The SpectraCell Micronutrient Test is a comprehensive blood test that measures the levels of various vitamins, minerals, antioxidants, and other essential nutrients within an individual's cells. This test can help treat chronic Lyme symptoms by identifying specific nutrient deficiencies that may be contributing to ongoing inflammation, fatigue, and cognitive issues often associated with this condition.

Vitamin C deficiency in chronic Lyme patients may weaken the immune system, making it harder for the body to fight infections and prolong inflammation. B vitamin deficiencies, particularly B1, B6, B9, and B12, can contribute to fatigue and cognitive difficulties often experienced in PTLDS patients by affecting energy production, neurotransmitter synthesis, and overall nervous system health. Finally, Vitamin D deficiency can negatively impact immune function, making the body more susceptible to infections and worsening inflammation-related symptoms, such as joint pain and arthritis in chronic Lyme.

Sleep Testing

The Sleep and Stress Panel by Ayumetrix measures “diurnal” (during the day) cortisol and melatonin. As stated above, many patients with chronic Lyme experience ongoing fatigue and sleep disorders. Using this test can help patients see if abnormalities in these hormones contribute to or impact their quality of sleep and stress levels.


Conventional Treatment for Chronic Lyme Disease

Conventional treatment for chronic Lyme disease is not universally agreed upon. While some medical organizations advocate for extended antibiotic treatment, others do not recommend additional antibiotics due to insufficient evidence of effectiveness and concerns about side effects or antibiotic resistance. The CDC states that patients usually get better over time and does not recommend any specific treatment.

Functional Medicine Treatment Protocol for Chronic Lyme Disease

Functional medicine addresses the root causes of illness and emphasizes the importance of personalized treatment plans. This approach can benefit individuals with chronic Lyme by incorporating non-pharmacologic interventions, dietary changes, and lifestyle modifications.

One non-pharmacologic intervention that may help alleviate PTLDs symptoms is cognitive-behavioral therapy (CBT). CBT aims to ease symptom burden and help patients manage the stress of living with a chronic illness. Mindfulness-based stress reduction (MBSR) has also shown promise in improving immune function. As noted above, stress contributes to immune system dysfunction, which may hinder chronic Lyme recovery.

Incorporating physical activity, such as a supervised resistance exercise program, has been shown to increase the number of days patients with persistent Lyme disease symptoms feel healthy and energetic. Regular exercise tailored to the individual's abilities can help enhance overall well-being and manage chronic Lyme symptoms.

Therapeutic Diet and Nutrition Considerations for Chronic Lyme Disease

Chronic Lyme disease can stem from various factors, such as inflammatory pathways or immune system dysfunction. The Mediterranean diet, renowned for its numerous health advantages, may help alleviate symptoms or improve a patient's condition due to its potential benefits in addressing these underlying causes. The Mediterranean diet emphasizes locally grown fruits and vegetables, healthy fats like olive oil and nuts, whole grains, fish, yogurt, and red wine.

The disease-fighting power of the Mediterranean diet is attributed to its ability to regulate inflammation by focusing on anti-inflammatory foods like berries, fish, and olive oil while excluding or limiting pro-inflammatory ones like red meat, sugar, and most dairy. This diet may also have a significant impact on reducing total mortality. Research has shown that certain foods can change the expression of pro-inflammatory genes and immune cells that drive disease.

While there is no specific diet for treating chronic Lyme disease, focusing on an anti-inflammatory diet like the Mediterranean diet can support the immune system, reduce inflammation, and improve overall well-being. By incorporating anti-inflammatory foods such as berries, fish, and olive oil and avoiding pro-inflammatory ones like red meat, sugar, and most dairy, individuals with chronic Lyme disease may experience improvements in their symptoms and overall health.

Supplements Protocol for Chronic Lyme

In addition to a healthy, balanced diet, lifestyle modifications, and stress reduction, certain supplements may benefit those experiencing symptoms associated with chronic Lyme.

Omega-3 Fatty Acids for Chronic Lyme Symptoms

Omega-3 fatty acids, particularly EPA/DHA, have anti-inflammatory properties that may help alleviate joint pain and inflammation associated with chronic Lyme. Numerous placebo-controlled studies investigating fish oil's effects on chronic inflammatory conditions demonstrate significant advantages, such as reduced disease severity and a decreased reliance on anti-inflammatory medications. As chronic Lyme may be caused by inflammatory pathways and may induce inflammation-based symptoms, fish oil supplementation may help reduce these symptoms.

Dose: Approximately 2,700mg/day (DHA+EPA) as studies on RA (rheumatoid arthritis, an autoimmune inflammatory condition) show anti-inflammatory effects at higher than average doses. It is important to note this is a higher-than-average dose recommended for RA patients, and it is not recommended for all patients.

Duration: Daily as symptoms continue; for general health promotion, the NIH suggests consuming 1.1-1.6 grams of omega-3 fatty acids a day

Cat’s Claw for Chronic Lyme Symptoms

Cat’s claw is commonly used for patients with symptoms of Lyme disease due to its antioxidant and anti-inflammatory properties. Cat's claw may help chronic Lyme patients by reducing inflammation and modulating the immune system. Cat's claw has demonstrated the ability to increase white blood cell count in human studies, which is crucial for a healthy immune response. It also promotes the production of lymphocytes and weakly activates B and T cells, while suppressing lymphoblasts. These effects contribute to a more balanced immune response, which may be beneficial for chronic Lyme patients. Cat’s claw’s anti-inflammatory and immune-modulating properties have the potential to provide symptomatic relief.

Dose: 60-300mg daily

Duration: 8-24 weeks

Garlic for Chronic Lyme Symptoms

Garlic may be beneficial in treating patients with Lyme disease symptoms due to its immune-boosting and antibacterial effects. Garlic may benefit chronic Lyme patients by addressing inflammation and oxidative stress, both of which are associated with the condition. Specifically, garlic contains sulfur-containing phytochemicals like allicin, diallyl disulfide (DADS), diallyl trisulfide (DATS), and S-allylmercaptocysteine (SAMC) that have been shown to modulate the immune system. Garlic supplementation has been found to lower circulating markers of inflammation (e.g., C-reactive protein and TNF-α) and oxidative stress (e.g., malondialdehyde), which could alleviate some symptoms experienced by chronic Lyme patients. Although direct evidence linking garlic to chronic Lyme disease treatment is lacking, its anti-inflammatory and antioxidant properties may provide symptomatic relief.

Dose: 2,400 mg daily

Duration: 12 months

Vitamin C for Chronic Lyme Symptoms

Vitamin C is a powerful antioxidant that plays a critical role in immune system function and overall health. Individuals with chronic Lyme may benefit from vitamin C supplementation as it can help boost immunity and combat the ongoing inflammation often associated with this condition. Vitamin C also supports the production and function of white blood cells, which are crucial for fighting off infections.

Dose: 500 mg/day; upper limit is 2,000 mg/day; the recommended daily intake is 75-90mg/day for adults

Duration: Daily as symptoms continue or daily for general health.

B Vitamin Complex for Chronic Lyme Symptoms

B vitamins play a vital role in energy production, brain function, and overall nervous system health. Research indicates that individuals with PTLDS often experience fatigue and cognition difficulties as a result of ongoing inflammation and imbalances in neurotransmitter production. B vitamin supplementation, particularly B1 (thiamine), B6 (pyridoxine), B9 (folate), and B12 (cobalamin), may help improve energy levels and cognitive function in individuals with PTLDS by supporting mitochondrial function, reducing inflammation, and promoting the synthesis of neurotransmitters essential for brain health.

Dose: Follow the recommended daily intake (RDI) on the supplement label or look for B Vitamin Complexes with minimum doses of the following B1: 1.2mg; B6 1.7mg; B9 400 mcg; B12 2.4mcg

Duration: Daily as symptoms continue or daily for general health. It is recommended to take the supplement in the morning as taking B vitamins can increase energy levels.

Melatonin for Chronic Lyme Symptoms

Melatonin is a hormone produced by the pineal gland that plays a crucial role in regulating sleep-wake cycles. Chronic Lyme patients often experience sleep disturbances, which can exacerbate fatigue, pain, and cognitive difficulties. Studies have shown that melatonin supplementation can improve sleep quality and duration in individuals with sleep disorders. By promoting better sleep, melatonin may help alleviate some of the symptoms associated with chronic Lyme, such as fatigue, pain, and cognitive issues.

Dose: 1-5 mg per day (as indicated by lab results), taken 30-60 minutes before bedtime.

Duration: If you have trouble sleeping for a brief period, you typically take melatonin for a duration of 1 to 4 weeks. However, some individuals may be prescribed melatonin for up to 13 weeks. If your sleeping difficulties persist even after you have completed your course of melatonin, it is recommended that you consult your doctor.

Vitamin D

Vitamin D plays a crucial role in immune system function and bone health. Studies show that this vitamin plays a vital role in immune system function, and deficiency has been linked to increased susceptibility to infections. Other studies show that low vitamin D levels often play a part in autoimmune and other chronic diseases, such as fibromyalgia, which has many similar symptoms to chronic Lyme. Furthermore, it has been shown that vitamin D supplementation reduces inflammation, which may help mitigate unpleasant symptoms such as inflammatory conditions such as joint pain and arthritis secondary to chronic Lyme.

Dose: 600-800 IU per day (people with or at risk for deficiency may need higher doses); as it is a fat-soluble vitamin, it can also be taken once a week

Duration: Daily


Probiotics are beneficial bacteria that support gut health and immune function. They may help restore the balance of gut microbiota disrupted by antibiotic treatment for Lyme disease. Research has demonstrated that specific probiotic strains, such as Lactobacillus and Bifidobacterium, can help modulate the immune response.

Dose: Look for products containing at least 1-50 billion CFUs (colony-forming units) and a variety of bacterial strains, including Lactobacillus and Bifidobacterium

Duration: Daily; a study testing the efficacy of probiotics in reducing infection risk showed benefit at 12 weeks

When to Retest Labs

Functional medicine practitioners typically retest labs after a period of 3 to 6 months to assess the progress of the treatment plan and make any necessary adjustments. This timeline can vary depending on the tests conducted and the individual's response to treatment.



Chronic Lyme disease, or PTLDS is a complex condition that requires a comprehensive, holistic approach to identify and address its root causes. Functional medicine offers a promising treatment protocol by focusing on optimizing immune function, reducing inflammation, and supporting the body's natural healing processes. Functional medicine practitioners can help individuals with chronic Lyme reclaim their health and improve their quality of life by utilizing targeted diagnostic testing, therapeutic dietary interventions, and evidence-based supplementation.

Resources That May Be Beneficial For You

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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