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A Functional Medicine Acute Lyme Disease Protocol: Testing, Diagnosing, and Treatment

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A Functional Medicine Acute Lyme Disease Protocol: Testing, Diagnosing, and Treatment

Lyme disease is an increasingly prevalent tick-borne illness affecting thousands of individuals every year. The Centers for Disease Control and Prevention (CDC) estimates roughly 476,000 people are diagnosed with Lyme disease in the United States annually. Lyme disease is a complex disease process and is often misunderstood. This article will delve into acute Lyme disease, including its symptoms, causes, diagnostic tests, and functional medicine treatment protocols to create a personalized treatment plan to recovery.


What is Lyme Disease?

Lyme disease is an infection transmitted to humans through the bite of infected black-legged ticks. The infection results from the bacteria spirochete Borrelia burgdorferi. Lyme disease can manifest in various stages, with symptoms affecting multiple organ systems, making diagnosis and treatment challenging.

What's the Difference Between Acute Lyme Disease and Chronic Lyme Disease?

Acute Lyme disease refers to the early stage of the infection, typically characterized by flu-like symptoms and the appearance of a bull's-eye rash called erythema migrans. If left untreated, acute Lyme disease can progress to chronic Lyme disease, also known as post-treatment Lyme disease syndrome (PTLDS), which presents with persistent symptoms such as fatigue, joint pain, and cognitive issues.

Acute Lyme Disease Symptoms

Common symptoms of acute Lyme disease include fever, chills, headache, muscle and joint aches, swollen lymph nodes, and the characteristic erythema migrans “bulls-eye” rash. Early detection is important in preventing the progression of acute Lyme to chronic Lyme disease.

What Causes Lyme Disease

Borrelia burgdorferi- the bacterium causing Lyme disease, is transmitted through the bite of infected ticks, also known as deer ticks or Ixodes ticks. When an infected tick feeds on a human or animal host, the bacteria can transfer from the tick's salivary glands into the host's bloodstream.

Environmental factors such as living in wooded areas or areas with tall grasses and vegetation can increase the risk of exposure to infected ticks. Additionally, outdoor activities like hiking, camping, and gardening can also raise the likelihood of encountering ticks. Geographic location is a major factor in Lyme disease transmission, as the disease is most commonly reported in the Northeastern, Mid-Atlantic, and North-Central regions of the United States (6).

Functional Medicine Labs to Test for Acute Lyme Disease

The CDC currently advocates for a two-tiered testing approach for diagnosing Lyme disease. No further testing is advised if the initial test yields a negative result. However, a second test should be carried out if the first test is positive or inconclusive (sometimes referred to as "equivocal"). The overall result is considered positive only if both the first test is positive (or equivocal) and the second test is also positive (or equivocal).

Lyme Disease Testing

Igenex Lyme Serology IgG & IgM is a great choice as the initial test for detecting Lyme disease. It measures the presence of antibodies against Borrelia burgdorferi, the bacterium responsible for Lyme disease. The test can help determine if your immune system has responded to an infection, indicating possible exposure to the bacteria. If the Igenex Lyme Serology test yields a positive result, further confirmation is needed through a test such as the Igenex Lyme Immunoblot IgG & IgM. This test offers a more specific analysis of the antibodies related to Lyme disease. As this test looks for specific protein bands associated with Borrelia burgdorferi, the immunoblot provides a higher degree of accuracy in confirming the diagnosis and guiding treatment decisions (6).

Testing for Co-Infections

Igenex Tick-Borne Disease Panel 8 is a test for identifying potential co-infections, as tick-borne diseases often occur alongside other infections. This comprehensive panel assesses eight common tick-borne pathogens that may coexist with Lyme disease, providing valuable information for a more accurate diagnosis and targeted treatment approach.

Functional Medicine Labs to Help Individualize Treatment for Acute Lyme Disease Patients

Various tests can help tailor treatment plans by identifying key factors impacting patients' health and recovery. These include:

Nutrient Testing

The Micronutrient Test by SpectraCell evaluates nutrient levels, including vitamins, minerals, and amino acids, to identify deficiencies that may impact immune function and recovery in acute Lyme disease patients. Identifying and addressing nutritional imbalances can play a crucial role in supporting the body's ability to fight infection and promote healing.

Stool Testing: Genova GI Effects Comprehensive Profile (3-Day)

Stool testing, such as the Genova GI Effects Comprehensive Profile, can be helpful in identifying potential co-infections and gastrointestinal imbalances in acute Lyme disease patients. This comprehensive stool analysis provides valuable information on gut microbiota, digestive function, and intestinal inflammation. As 70%-80% of the immune system is found in the gut, identifying potential imbalances can help strengthen the immune system.

It’s important to note that if patients are undergoing treatment with antibiotics, antiparasitics, antifungals, or taking probiotic supplements, it is advised to wait at least 14 days after the final dose before starting the test; a waiting period of 28 days may be more suitable after completing antibiotic therapy.


Conventional Treatment for Acute Lyme Disease

Conventional treatment for acute Lyme disease typically involves antibiotics, such as doxycycline or amoxicillin, to target the B. burgdorferi infection.

Functional Medicine Treatment Protocol for Acute Lyme Disease

A comprehensive functional medicine approach to acute Lyme disease incorporates a therapeutic diet, nutritional support, and targeted detoxification strategies to bolster the immune system and facilitate recovery.

Therapeutic Diet and Nutrition Considerations for Acute Lyme Disease

For those dealing with acute Lyme disease, it's essential to create a diet plan that focuses on strengthening the immune system and providing the necessary nutrients for recovery. Including immune-boosting and nutrient-rich foods in the diet can make a significant difference. Foods high in omega-3 fats, such as fatty fish (tuna, herring, mackerel, salmon, sardines, and trout), can help improve immune function and reduce inflammation.

Eating citrus fruits like oranges, lemons, limes, and grapefruits provides vitamin C, which can support immune cell functions and potentially prevent or shorten infections. Additionally, incorporating garlic, ginger, and turmeric into meals can offer antioxidant and anti-inflammatory benefits, further supporting the immune system's response. A well-rounded diet for acute Lyme disease patients should also emphasize foods that are high in vitamins and minerals, such as broccoli, bell peppers, spinach, yogurt, almonds, and sunflower seeds. These foods supply essential nutrients like vitamins A, C, E, and others that play vital roles in maintaining overall health and boosting the immune system. One great nutrient-dense diet that follows many of these suggestions is the Mediterranean diet (20,21).

Supplements Protocol for Acute Lyme Disease

Several supplements are recommended to help patients recover from Lyme disease. Below are many supplements used in clinical practice.

Probiotics for Acute Lyme Disease

Probiotics can be used to help restore healthy gut flora, which may be compromised by antibiotics used for the treatment of Lyme disease or in patient’s experiencing co-infections. Restoring healthy gut bacteria can help improve immune function and help speed recovery.

Dose: 10 - 20 colony-forming units/day

Duration: Studies have shown changes in the microbiome after supplementing with probiotics for one month.

Coq10 for Acute Lyme Disease

Coenzyme Q10 (CoQ10) supplementation may help alleviate Lyme disease symptoms by targeting the underlying pathogenic mechanisms. CoQ10 is involved in mitochondrial function and has anti-inflammatory and antioxidant properties. These attributes can reduce oxidative stress and fatigue in patients with Lyme disease, making CoQ10 a potential supplementary treatment option.

Dose: Common daily dosage falls between 100-200 mg

Duration: As symptoms persist or ongoing for general health.

Vitamin C for Acute Lyme Disease

Vitamin C is a potent antioxidant vital to immune system performance and general well-being. Those affected by Lyme disease may benefit from supplementing with vitamin C, which can enhance immune response. Furthermore, vitamin C assists in the creation of white blood cells, which play an essential role in combating infections.

Dose: 1 g/day

Duration: As symptoms persist.

Cryptolepis Sanguinolenta

Cryptolepis sanguinolenta, traditionally used in Ghanaian medicine for treating malaria, has shown potential for alleviating acute Lyme disease symptoms. Notably, cryptolepis displays potent activity against both growing and non-growing B. burgdorferi. In subculture studies, 1% cryptolepis sanguinolenta extract led to complete eradication, outperforming doxycycline, cefuroxime, and other active herbs. For acute Lyme disease patients, cryptolepis sanguinolenta may help reduce symptoms through its anti-inflammatory and immune-modulating properties, as well as its activity against B. burgdorferi.

Dose: 1% cryptolepis sanguinolenta extract

Duration: As symptoms persist.

When to Retest Labs

The formation of antibodies to combat Lyme disease-causing bacteria typically requires several weeks. Consequently, tests conducted earlier than this period might yield negative results. In such instances, retesting the person after a few more weeks should produce a positive outcome if they have Lyme disease. For other more general labs, retesting is typically recommended 6-12 weeks after initiating treatment to assess and adjust the treatment plan as needed.



Acute Lyme disease is a complex condition that requires prompt diagnosis and treatment to prevent progression to chronic Lyme disease. Understanding the differences between acute and chronic Lyme disease, as well as exploring functional medicine approaches to diagnosis and treatment, can lead to better patient outcomes. By incorporating a nutrient-dense, anti-inflammatory diet, targeted supplements, and personalized lab testing, functional medicine practitioners can develop a comprehensive treatment plan to address the root cause of acute Lyme disease and support recovery.

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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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