People around the world understand that insects carry disease. Mosquitos make most of the headlines, especially in developing countries. Malaria, yellow fever, and Zika are all very real risks in many parts of South America, Africa, and Asia. (15)

Here in North America, those diseases are fairly contained. However, while mosquitos are more of an annoyance, cases of tick-borne diseases, including babesiosis, anaplasmosis, and most commonly, Lyme disease, grow every year. (4) I have spent the majority of my medical career learning about the underlying bacterial infection (Borrelia burgdorferi), the signs of Lyme disease, and most importantly, how to treat Lyme disease.

practitioner removing a tick from woman's neck

Make sure you know how to remove the tick correctly! Please don’t use a flame or vaseline to remove it!

What is Lyme disease?

Broadly speaking, there are two stages to Lyme disease: “acute” and “chronic”. Though they are the same bacteria, they may as well be totally different pathogens. (14)

Acute Lyme disease

The symptoms of acute Lyme disease include the quintessential “bulls-eye rash” and flu-like symptoms. (9)

If you’re lucky enough to spot Lyme during its acute phase, it’s commonly treated with a four to six-week round of antibiotics (not a one-day course, not a 14-day course, but a full 28 to 42 days). (8) Talk to your healthcare practitioner, ideally a Lyme-literate physician, about medications. In addition to prescriptions, it will be important to support your system with natural solutions such as:

  • A probiotic to protect the good bacteria (microbiome) in your gut from the effects of the antibiotic; probiotics may reduce side effects associated with antibiotic use, such as diarrhea and other gastrointestinal issues. (6)(13)
  • A liver/detox supplement to help clear out toxins and support your liver when on medications; liver detoxification protocols have been shown to improve Lyme related symptoms. (7)
  • An immune-boosting supplement to help your immune system fight this infection on its own; certain supplements have anti-inflammatory and immune-enhancing effects. (7)(10)
  • A multi-vitamin/multi-mineral to make sure your body is getting the basic nutrients it needs during this time; multi-vitamin/multi-mineral supplements can decrease the risk of nutrient deficiencies and replenish nutrients you may be missing in your diet. (2)

Here’s the problem: while the bull-eye rash is found in 99% of internet searches for Lyme disease, it actually appears in less than 50% of patients (only 34% in a big data study). (12) And those flu-like symptoms? They can be easily mistaken as… the flu. If the initial infection goes untreated, that’s when acute Lyme transforms into a complex and dangerous monster called chronic Lyme.

Chronic Lyme disease

When an acute tick bite goes unnoticed, the bacteria starts to wander. It travels throughout the body, finding homes in the brain, heart, gut, and joints. It can do this because Borrelia burgdorferi is a special type of bacteria. The technical name for this type of bacteria is a spirochete. This spiral-shaped bacteria has several appendages that wind around a cell body and mimic the structure, blending in almost seamlessly. The most common cells targeted are neurons in the brain, the smooth muscle cells of the heart, and connective tissues (ligaments and tendons). Once locked onto a cell, the spirochete begins to multiply and wreak havoc.

Because of its adaptability, Lyme can mimic many chronic diseases, such as rheumatoid arthritis, multiple sclerosis, or chronic fatigue syndrome. If your healthcare providers are looking for any of those diseases, they won’t find them. Sadly, many patients go undiagnosed for years, or even decades, with symptoms that don’t show up on lab results. (12)

Health issues related to Chronic Lyme

Here is a breakdown of some of the most common symptoms found in chronic Lyme disease.

Brain fog

The Lyme bacteria can infect the brain causing significant inflammation and damage. Often called “brain fog” because it’s described as your brain moving through a haze, symptoms include:

  • An inability to find words or think clearly about subjects patients know well
  • Headaches
  • Neuropathy
  • Poor short-term memory and poor concentration
  • Tinnitus
  • Vertigo
  • Vision changes (11)

Joint pain

Often early in the disease, the bacteria will disseminate into the joint pain and cause arthritis or inflammation of the joints. There can also be swelling of the joints and synovial fluid (synovitis). (1)

Severe fatigue

One of the most common and debilitating symptoms is fatigue. This fatigue is not the satisfying ‘I’m tired from a long day’ type of tired. It’s a draining, all-consuming level of tiredness that hits quickly. It feels more like, “I just took a shower, and now I need to sit down to rest because that wiped me out.” It’s believed that Lyme-related fatigue is likely a combination of brain inflammation, an overly stressed immune system, mitochondrial depletion, and toxin burden. (7)


Most outsiders chalk up a patient’s depression to them complaining excessively about their other symptoms (creating its own depressive spiral, ironically). The reality is that brain inflammation caused by the bacteria is actually irritating the neural network, causing a depressive response. There are over 400 peer-reviewed articles addressing neuropsychiatric symptoms caused by Lyme. Fix the Lyme, and the depression goes away. (3)

How to treat Lyme disease, naturally

Chronic Lyme is a complex issue that requires medical detective work and time to unravel. No two cases are identical. Functional and integrative practitioners are especially well equipped to take a whole-systems approach to care, find all the places where Lyme is hiding, and develop treatment protocols to address each infestation. This includes looking at your diet, exercise routines, sleep habits, and stress management tools. The good news is that once identified there are several treatments, including many natural treatments, for Lyme that can help fight off the bacteria while boosting your own immune system.

practitioner giving a patient a supplement bottle

Probiotics are often recommended by integrative practitioners to support the gut and rebuild the microbiome.

Natural supplements play a large role in helping to halt and reverse some of the damages done by the bacteria. Other supplements support the immune system, allowing a patient to develop enough strength to fight off the disease on their own.

Antimicrobials and immune support

While we use antibiotics like minocycline and disulfiram, we also leverage herbs such as Cat’s Claw and Japanese Knotweed. Recent studies have shown what herbalists have known for years – these antimicrobial herbs work! (5)

Strengthening the immune system to fight off the infections without outside help is arguably more important than attacking the infection. At our clinic, we utilize many different options to boost the immune system, such as ozone, nutritional IVs, and peptides to support the immune system. (5)

Probiotics and other support supplements

Coupled with those treatments, we recommend probiotics to support the gut and rebuild the microbiome, as well as milk thistle to support the liver. We also use a combination of green tea extract, turmeric, skullcap, resveratrol, chamomile, and luteolin to lower neurological inflammation. (13)

The bottom line

There is no cure for Lyme disease, but by creating plans to combat individual constellations of issues, we can push Lyme into full remission. Lyme is often misdiagnosed and misunderstood. For patients suffering from this chronic infection, there is hope and, using a functional medicine approach, individuals can get better.

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  1. Arvikar, S. L., & Steere, A. C. (2015). Diagnosis and treatment of Lyme arthritis. Infectious Disease Clinics of North America, 29(2), 269–280.
  2. Blumberg, J., Frei, B., Fulgoni, V., III, Weaver, C., & Zeisel, S. (2017). Impact of frequency of multi-vitamin/multi-mineral supplement intake on nutritional adequacy and nutrient deficiencies in U.S. adults. Nutrients, 9(8), 849.
  3. Bransfield, R. C., Aidlen, D. M., Cook, M. J., & Javia, S. (2020). A clinical diagnostic system for late-stage neuropsychiatric Lyme borreliosis based upon an analysis of 100 patients. Healthcare, 8(1), 13.
  4. Centers for Disease Control and Prevention. (2019, April 22). Prevention is key in fight against Lyme and other tickborne diseases. Retrieved from
  5. Feng, J., Leone, J., Schweig, S., & Zhang, Y. (2020). Evaluation of natural and botanical medicines for activity against growing and non-growing forms of B. burgdorferi. Frontiers in Medicine, 7(6).
  6. Heta, S., & Robo, I. (2018). The side effects of the most commonly used group of antibiotics in periodontal treatments. Medical Sciences, 6(1), 6.
  7. Horowitz, R. I., & Freeman, P. R. (2018). Precision medicine: The role of the MSIDS model in defining, diagnosing, and treating chronic Lyme disease/post treatment Lyme disease syndrome and other chronic illness: Part 2. Healthcare, 6(4), 129.
  8. International Lyme and Associated Diseases Society. (2019, April 16). Treatment guidelines. Retrieved from
  9. International Lyme and Associated Diseases Society. (2020, February 18). Lyme disease basics for providers. Retrieved from
  10. Lantos, P. M., Shapiro, E. D., Auwaerter, P. G., Baker, P. J., Halperin, J. J., McSweegan, E., & Wormser, G. P. (2015). Unorthodox alternative therapies marketed to treat Lyme disease. Clinical Infectious Diseases, 60(12), 1776–1782.
  11. Lyme Disease Action. (2013, May). Lyme neuroborreliosis. Retrieved from
  12. (2019, August 1). MyLymeData chart book released. Retrieved from
  13. Rodgers, B., Kirley, K., & Mounsey, A. (2013). Prescribing an antibiotic? Pair it with probiotics. Journal of Family Practice, 62(3), 148–150.
  14. Shor, S., Green, C., Szantyr, B., Phillips, S., Liegner, K., Burrascano, J., Jr., … Maloney, E. L. (2019). Chronic Lyme disease: An evidence-based definition by the ILADS Working Group. Antibiotics, 8(4), 269.
  15. World Health Organization. (2016, October 17). Mosquito-borne diseases. Retrieved from