A Functional Medicine Guide To Lyme Disease: Symptoms, Natural Remedies + What Your Doctor Isn’t Telling You


Lyme disease is no joke. It has spread rapidly across the country in recent years due to the rise in tick populations around the country. In fact, according to the National Institutes of Health, incidences of Lyme disease have surged by 320 percent (1) since the ’90s. The CDC even suggests (2) that the number of Lyme disease cases may be 10 times higher than the officially reported number, with an estimated 300,000 incidences each year in America.

The rising numbers and its growing impact on people's health, have led the CDC to officially categorize (3) Lyme Disease as a chronic health problem. While conventional medicine traditionally focuses on alleviating symptoms with antibiotics, as a functional medicine practitioner, it is my job to uncover everything about this insidious disease to better identify and treat Lyme disease. Read on to learn everything you need to know about Lyme disease, its risk factors, and natural ways you can finally achieve long-term, sustainable healing from this condition.


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What is Lyme Disease?

Lyme Disease is a bacterial infection caused by transmission of the Borrelia burgdorferi bacteria when humans are bitten by an infected tick. These parasites are often so tiny that most people don’t see them or even notice the bite. Depending on where you live it could be:

  • An infected blacklegged tick or deer tick, in the northeastern and central U.S.
  • An infected western blacklegged tick, on the West Coast of the U.S.
  • An infected sheep tick, in parts of Europe.

Lyme is often referred to as “The Great Imitator” (4) because its symptoms can mimic many other diseases like chronic fatigue syndrome, fibromyalgia, multiple sclerosis, and dementia. Some researchers even theorize whether Lyme could actually be a trigger for some of those diseases. Sadly, partly for this reason, people with Lyme are often told that it’s all in their head, or that they’re simply “just depressed.” 

In acute Lyme, within about a month of a bite, the symptoms may include:

  • Fatigue
  • Flu-like symptoms including fever, hot flashes, and chills
  • Joint pain
  • Back pain
  • Headaches
  • A red “bull’s-eye” rash around the site of the bite

To hear more about living with Lyme disease, listen Jedediah’s story here

The Problem with Lyme Disease Conundrum

Unlike other infections, Lyme disease is difficult to detect and even harder to recover from - even after antibiotics. As a functional medicine practitioner, here’s what I wish more people knew about Lyme disease and what makes it such an elusive condition.

1. The Lyme bacteria is a survivor

Lyme bacteria knows how to stay alive inside its host. It suppresses the immune system, which allows it to survive and multiply. Lyme also seems to have the ability to “cloak” itself, making itself invisible to our immune system. In fact, Borrelia is so smart that some research (5) suggests that when it senses it’s being attacked, it can go into a dormant state, allowing it to live and survive against the onslaught of antibiotics. Other studies suggest (6) that Borrelia can actually mutate its own genes to make it resistant to antibiotics.

2. Diagnosis is tricky

Only about half of all Lyme patients actually remember getting a tick bite. Plus, the classic “bull’s-eye” rash that people associate with Lyme may not appear in all cases, or may appear somewhere the victim never sees, such as on the scalp, hidden by hair. Some research (7) suggests that conventional Lyme tests may not be sensitive enough to make an accurate diagnosis, especially during the later stages of disease. False-negative results are also common.

3. Conventional treatment may not be sufficient

The conventional approach to Lyme typically includes 10 to 28 days of antibiotics. Then what? Well, nothing. That course of antibiotics supposedly kills off the bacteria. The problem with this is that some research (8) suggests that as many as 25 percent of patients with Lyme disease still have some symptoms long after antibiotic therapy, suggesting that some bacteria lingers, or its effects linger in the body.

Risk factors for developing Lyme disease

Due to Lyme disease’s insidious nature, researchers are constantly learning more about this condition. The mechanisms of how it works and why some people get infected over others is still being studied with new information coming out every day. However, there are some factors that are definitively known to increase your risk of developing Lyme disease.

1. Genetic variants

Even though Lyme disease itself isn’t genetic, there are certain genes that can make you more susceptible to this condition. While more research needs to be done on the specific mechanisms behind genetic variants and Lyme disease, studies have shown (9) that certain HLA gene variants like such as HLA-DRB10401, might be associated with an increased risk of developing Lyme disease or experiencing more severe symptoms if infected.

Learn more about HLA gene variants here.

2. Blood types

It may be worth finding out your blood type, if you don’t know it already as new research shows that ticks tend to prefer type A blood the most, followed by type 0, type AB, and then type B. In fact, a study published in Annals of Agriculture and Environmental Magazine, (10) found that 36 percent of ticks preferred type A blood whereas only 15 percent of ticks liked type B. 

Listen to my episode of The Art Of Being Well to learn more about blood types and tick bites.

3. Location and detection

Where you live is one of the more obvious contributing factors to contracting Lyme disease. If you live or spend time in wooded areas or grasslands where ticks tend to live your likelihood of coming across a tick that carries the Borrelia burgdorferi bacteria is automatically higher as up to 50% of ticks in certain locations can carry this bacteria. Also, according to the CDC, (11) a tick must be attached between 36-48 hours before the Borrelia burgdorferi bacteria can be transmitted. Therefore, early detection is vital in order to remove a tick as quickly as possible - ideally within 24 hours. 

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A functional medicine approach to Lyme

As a functional medicine practitioner, my approach to Lyme is different. Here’s what I recommend:

1. A detailed health history

Step one is a detailed health history. When I do this with my patients, I ask all kinds of nosy questions. (One patient asked me if I was in the KGB! No, ma’am, just getting to the root issues!) If you think you could have Lyme disease, schedule a telehealth consultation with my team to get this conversation started.

2. Comprehensive labs

It’s important to catch Lyme as early as possible, so it doesn’t become chronic. The sooner it is treated, the more likely antibiotics will be able to eradicate it all. In addition to using the two conventional tests accepted by the CDC, Elisa and Western Blot labs, I also often screen clients with these labs:

  • CD57+/CD8-Absolute count: At this point, we believe that only Lyme bacteria will depress the CD-57, so someone with a high CD-57 is probably sick with something other than Lyme.
  • C4a: This is another blood test to assess the immune system. Chronic Lyme disease could be associated with increased levels of C4a.

We might also consider other tests to dig a little deeper.

3. Support healthy biofilms

Biofilm is a thin, slimy film of bacteria that adheres to a surface. Biofilms are not inherently bad, they are simply a way that bacteria colonize. It’s the composition of the biofilm that makes it probiotic or pathogenic. Functional medicine’s goal is to promote a healthy biofilm through foods, lifestyle changes, and natural medicines. Some natural biofilm-modifying tools I might recommend include:

  • Colostrum/Lactoferrin supplements: Lactoferrin inhibits pathogens and promotes healthy biofilms.
  • Probiotics and prebiotics: These promote probiotic balance.
  • Enzymes: These break down biofilm.
  • Xylitol: This is a natural (12) anti-biofilm.
  • EDTA: This is a strong anti-biofilm.

I recommend talking to your health care practitioner about what might help support your health.

4. Address microbiome issues

At least 70 percent of your immune system is in your GI tract, and the microbiome is a foundational part of immune health. Addressing any underlying gut dysfunctions, such as candida overgrowth, could help to strengthen your immune system to fight off infections.

5. Integrate natural medicines

I typically suggest immune support formulas including herbs and compounds such as Siberian ginseng, samento, sarsaparilla, guaiacum, (13) astragalus, resveratrol, and cat’s claw. One study also suggests (14) that stevia could be as effective as antibiotics in treating Lyme disease.

6. Consider antibiotics

Some functional medicine practitioners will suggest conventional antibiotics to reduce total bacterial load. For example, ILADS recommends (15) 100 to 200 mg of doxycycline twice daily for a minimum of 20 days for all tick bites where there is evidence of tick feeding.

7. Address any co-infections

I also test my patients for viruses such as EBV (Epstein-Barr virus), HSV 1&2 (Herpes simplex viruses 1&2), HHV-6 (Human Herpes virus), and CMV (Cytomegalovirus). These viruses can put more stress on the immune system. In my clinic, I find that olive leaf, larrea tridentata, bee propolis, Melissa officinalis, L-lysine, zinc, and vitamin C can be good antiviral support options.

Learn more about EBV on my episode of The Art Of Being Well.

8. Support genetic weaknesses

Certain genes can predispose certain people to chronic infections. I recommend looking for methylation gene changes like MTHFR mutations and supporting the body’s methylation and detoxification pathways.

Lyme Disease Diet: How are they connected?

We’re starting to realize that our modern lifestyles are not doing us any favors when it comes to Lyme- That’s where lyme disease diet comes into play.

You see, our genetics as humans haven’t changed in over 10,000 years, but the world around us has changed greatly. Factors like processed foods, soil nutrient depletion, and air and water pollution are all likely amplifying and perpetuating the impact that chronic infections caused by viruses, mold, protozoa, and bacteria (like Lyme disease) have on the body. At first this might seem like bad news, but the truth is if certain environments and lifestyle factors can make us more vulnerable to Lyme, certain lifestyle factors and environments can also make us less vulnerable, too. A lyme disease diet could make all the difference .

What’s wrong with the way our healthcare system treats Lyme?

So how does mainstream medicine diagnose and treat Lyme? Most of the time it’s done through lab work and a round of antibiotics - but that’s only if you notice a bite or your doctor has been trained to recognize the many vague and mysterious symptoms of Lyme. And even if you do successfully treat Lyme, chronic Lyme can persist long after you’ve taken those antibiotics, a condition that is now referred to as post-treatment Lyme disease syndrome. Thankfully, post-treatment Lyme disease syndrome is gaining recognition, especially in the functional medicine community and with the support of organizations like the International Lyme and Associated Diseases Society.

As a Lyme-literate functional medicine expert, I take a multi-pronged approach to treating Lyme disease. This includes specific supplements, forms of exercise, and most importantly: using food as medicine - a focus on a successful lyme disease diet.

Can a keto diet support your ability to heal from Lyme?

In my practice, dietary recommendations for Lyme often takes the form of a mostly plant-based ketogenic diet, which I call the Ketotarian diet. The Ketotarian diet avoids the common downsides and risks of the conventional keto diet (AKA, eating a ton of meat and diary), while still allowing you to take advantage of the benefits of nutritional ketosis to fend off Lyme disease and get you back to optimal health.

1. It supports healthy methylation pathways

Certain genetic factors can make you more vulnerable to falling ill from Lyme disease - one of these is the MTHFR gene mutation which impairs methylation. This is a problem because methylation helps control the health of your hormones, inflammatory pathways, and detox pathways - which all help you manage Lyme. The Ketotarian diet is a great way to support healthy methylation. Certain foods like leafy greens and cruciferous veggies acts as extra credit since they are rich in folate and sulfur compounds that directly support methylation. Talk about food as medicine at its best!

2. It helps boost mitochondrial health

Research shows that oxidative stress can harm the mitochondria in the immune cells of Lyme patients, which results in extreme fatigue. A ketogenic diet for lyme disease can combat this by increasing (16) mitochondrial biogenesis (AKA, the production of new mitochondria), which happens by way of autophagy. Autophagy is a process in the body that helps remove damaged cells; (17) it’s essentially your body’s own cleaning system. If you want to take things to the next level, you can follow an intermittent fasting plan in combination with your keto diet. Fasting also causes ketosis and is another way to increase autophagy.

3. It combats chronic inflammation

As I mentioned before, when you’re exposed to Lyme disease over a long period of time, it can trigger autoimmune diseases. (18) To reverse this (Or prevent it in the first place!), it’s imperative that you reduce inflammation in your body. Luckily for us, the ketones produced when your body is in ketosis are anti-inflammatory. In one example, the ketone beta-hydroxybutyrate acts as a signaling molecule and epigenetic modulator, working to activate (19) anti-inflammatory pathways (such as AMPK and Nrf-2) and inhibiting inflammatory pathways like NFkB, COX2, and the NLRP-3 inflammasome.

In plain English, this means that a plant-based ketogenic diet for lyme disease attacks chronic inflammation in multiple ways making it one of the best diets to cure lyme disease naturally. This, combined with restored mitochondrial function, can help eliminate debilitating neurological symptoms like brain fog, which often occur with chronic Lyme. Sounds pretty good, doesn’t it?

4. It restores the microbiome to its former glory

Most Lyme experts can agree on one thing: The gut microbiome is a key player in fighting off Lyme infections. This is because about 80 percent of our immune system is located in your GI tract. The good news is that the combination of healthy fiber and probiotic foods on the Ketotarian diet will help bring balance to your microbiome by killing bad bacteria and inoculating your belly with healthy ones (called probiotics) that help boost the immune system, lower inflammation, and fight disease. The Ketotarian diet is also low in sugar and carbs, foods that are known for promoting inflammation and suppressing immune function.

To learn more about how to best protect your gut, read The Definitive Functional Medicine Guide To All Things Gut Health.

Is the Keto Lyme Diet the answer?

More studies need to be done that test this diet on patients with Lyme, but for now I feel it’s a safe and effective way to support your body through the process of healing Lyme. Many of the pathways implicated in Lyme disease are also modulated with a high-fat, low-carb keto diet. Because of this, in my practice I put almost all my patients with Lyme on some form of Ketotarian diet. Depending on how severe your Lyme disease is, I suggest seeking out a Lyme-savvy functional medicine practitioner who’s familiar with Lyme and low-carb, high-fat diets like the Keto diet.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.

Photo: unsplash.com

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  1. Kugeler, K. J., Farley, G. M., Forrester, J. D., & Mead, P. S. (2015). Geographic Distribution and Expansion of Human Lyme Disease, United States. Emerging Infectious Diseases, 21(8), 1455-1457. https://dx.doi.org/10.3201/eid2108.141878.
  2. CDC provides estimate of Americans diagnosed with Lyme disease each year August 19, 2013 https://www.cdc.gov/media/releases/2013/p0819-lyme-disease.html
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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

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