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Functional Medicine & Lyme Disease

Written by

Deborah Freudenmann BHSc

“I have just been diagnosed with Lyme disease. I don’t know where to begin?”

“I have Lyme disease, is there something natural I can do?”

“I’ve been struggling with Lyme disease for years; I’m desperate”

“This isn’t the life I imagined for myself, I’m constantly at war with my body: Lyme disease”

These are just some of the common headlining emails I’ve received over the past few months. If Lyme disease impacts you, a friend, family member or loved one then this article is for you.

In this article you will learn what Lyme disease is, it’s presentations and developments, co-infections and finally the functional medicine approach to this disease.

“Lyme disease, where to begin – it feels like it comes out of nowhere and is determined to stay forever. The physical, emotional and mental challenges that we faced every single day is hard for outsiders to truly understand. There is a constant difficulty in doing everything. Sometimes this disease forces you to stay up all night. You suffer from swollen lymph nodes which is beyond painful, you feel fatigue like you’ve never felt before, there is a constant headache, your muscles and joints ache which makes it hard to stand up. Lyme disease feels like your body is constantly at war”

Lyme disease, or borreliosis, is a common vector-borne disease that occurs due to the bacterium Borrelia burgdorferi. In rare cases, Lyme disease may occur due to being infected by Borrelia mayonii. Lyme disease is a multisystem infection that often goes undiagnosed or misdiagnosed. The Centers for Disease Control and Prevention reports that up to 300,000 new cases of Lyme disease are diagnosed a year. Considering how often Lyme disease goes undiagnosed or misdiagnosed, this number is likely a wild underestimation!

The role of biotoxins in the development of Lyme disease

Biotoxins refer to a group of substances, which are biological in nature yet they are toxic to humans.
Biotoxins that are produced by bacteria (often released by the tick-borne microbes) can produce a wide range of adverse effects on the human body, by targeting different tissues.

They contribute to a silent crisis and can cause long-term damage to different issues like muscles, nerves or organs.

Acute vs chronic Lyme disease

Acute Lyme disease usually presents as flu-like symptoms with a distinctive rash shaped like the ‘bull’s eye’ at the site of the tick bite.
Lyme disease can be managed more easily at this early acute stage. A course of antibiotics can sometimes clear up the infection in a shorter duration, or a fever can manage to deal with the majority of bacteria.

Complications usually arise when the infection turns chronic. Chronic Lyme diseases occur when the bacteria have been fully integrated into the patient’s body, making them harder to eliminate.

Once chronic Lyme disease sets in, the flu-like symptoms subside. Slowly, patients may develop more intense symptoms such as loss of memory, cognitive impairment, numbness or tingling in the arms and feet, and chronic fatigue.
These symptoms can affect the patients for years after the infection is diagnosed and treatment is started.

Ticks infect humans during the feeding stage

Ticks transmit Borrelia burgdorferi (as well as many other pathogens) during the feeding process:

  1. Once a tick lands on a human, it attaches to the skin and starts secreting a numbing agent that prevents the host (YOU) from feeling the bite.
  2. When the tick bites into the skin, it inserts a feeding tube and releases another substance which allows it to attach firmly to the skin during feeding
  3. The tick slowly sucks blood from the host over several days before falling off

If the tick contains any pathogens these would be transmitted to you during the feeding process.

What are the stages of Lyme disease?

The development of Lyme disease occurs in 3 stages.

  1. The first stage is the early localized stage during which the symptoms are limited to a part of the body.
  2. The second stage is the early disseminated stage. This stage develops several weeks after the tick bite as the bacteria begin to spread throughout the body.
  3. The third stage is called the late disseminated stage. It develops when the bacteria have spread throughout the body leading to serious impairment of the functions of the vital organs including the heart, nerves, and brain.

What are the symptoms of chronic Lyme disease?

The common symptoms of chronic Lyme disease include:

  • Frequent headaches
  • Vertigo and dizziness
  • Pain in the joints
  • Neuropathy
  • Migrating pains that come and go in the joints and tendons
  • Sleep disturbances
  • Immune dysfunction and inflammation
  • Irregular heart rhythm
  • Pain and stiffness in the neck
  • Confusion and mental fogginess
  • Depression, anxiety, mood swings, cognitive dysfunction
  • Numbness in the arms and legs
  • Severe fatigue
  • Alzheimer’s disease

Types of co-infections and symptoms

Patients with Lyme disease are more likely to suffer from co-infections such as Babesia, Bartonella, Ehrlichia, and Rickettsia. Ticks can often carry several other pathogens such as bacteria, viruses and parasites. Some of the organisms in ticks are not pathogenic but they can still create a more favourable environment for Lyme disease. Other tick-borne organisms are pathogenic and can cause their own symptoms and complications.

Regardless, these are opportunistic infection that occur due to extreme weakness and poor immunity caused due to the widespread damage to organs and tissues and the impairment of physiological functions in patients with Lyme disease.

Lyme disease is a moving and changing target

The greatest challenges in treating Lyme disease arise due to the crafty nature of this infection.

Borrelia burgdorferi impairs the immune system – specifically the part of the immune system that enhances the ability of engulfing bacteria and other small particles. Unfortunately, without a proper functioning immune system this not only opens up the body to opportunistic infections as mentioned above but also allows Borrelia to persists within the body.

Borrelia burgdorferi also possesses an ability to transform its own change shape and design to evade the immune system (an immune system which is already compromised). In addition to this, Borrelia also teams up with other microorganisms such as co-infections to create a biofilm. This means that when bacteria are incorporated into a biofilm, they are more resistant to antibiotics.

Functional Medicine & Lyme

The functional approach to the management of Lyme disease is aimed at stimulating the body’s own defence mechanisms to activate a healing and repair process which ultimately restores health. Our goal is to treat the patient and not just the infection. As Lyme disease is a multisystem infection there are many factors that need to be addressed.

  • Modulate the inflammatory-immune response
  • Address the infection and co-infections
  • Check for mould exposure
  • Supporting detoxification pathways
  • Determine nutrient deficiencies and provide nutrient support
  • Addressing the mental and emotional factors (stress management)
  • Support intestinal dysfunction and overall gut health

Hyperthermia treatment

Hyperthermia treatment is highly recommended for the management of acute and chronic Lyme disease.

The body core temperature is raised to about 39.5 C, which simulates a natural fever and causes an increase in the number and activity of natural cells, T-helper cells and cytotoxic T-cells.

Research studies have demonstrated that the growth of the strains of bacteria that cause Lyme disease could be impaired at a temperature of 37 degrees C. It is further inhibited when the body temperature is raised to 39 to 40 degrees C.

This means the bacteria are unable to survive when the body temperature is increased during hyperthermia treatment. This temperature does not kill Borellia but it flags them with heat shock proteins so they become visible to the immune system.

During fever your body flushes out new white blood cells (killer cells) which help deal with the infection. The increased oxygen availability during fever, more white blood cells and the fact that your pathogenic bacteria are flagged all work in favour of the patient.

Hyperthermia may be particularly beneficial for patients being treated with antibiotics as it might allow the infection to clear faster.

Ozone therapy

Ozone treatments reduce the overall infection and can help to relieve some of the underlying causes of Lyme disease.

Increased oxygen supply during ozone therapy would help with detoxification, destroy bacteria and viruses, cleanse the abnormal blood cells, promote cellular metabolism for greater energy and ATP availability, and enhance blood circulation.

Due to the up regulation of NrF2 (antioxidants) ozone also triggers the production of antioxidants including glutathione peroxidase (master antioxidant) which are all necessary enzymes to protect healthy cells from being infected. The more your antioxidant status is unregulated the more immune you become to renewed self-infection and overgrowth. This process is slow and requires weeks of treatments but it is worth the effort in the long run.

These benefits of ozone therapy would help you feel energetic and provide significant relief from the symptoms of Lyme disease.

There was a case report of acute bacterial infection – tick bite cellulitis, which immediately responded to ozone therapy as the sole treatment, and which fully resolved within 24-48 hours. Ozone therapy could be considered as an adjunctive or alterna- tive therapy for bacterial infection.

Anti-inflammatory diet and supportive nutrients

Due to the extra burden of additional bacteria feasting on your reserves all Lyme patients are in general vary depleted in various vitamins, minerals and amino acids. An exact panel of deficiencies will help with supplementation and regulation.

In several clinics that treat Lyme disease very effectively we found that the importance of proper supplementation was crucial for their success.

Your diet should contain of lots of wholefoods – good quality protein, fats and plenty of vegetables!

There are countless supplements (herbs, nutrients) which can benefit an individual with Lyme disease. Depending on the progression of the disease and the individual – there is no generalised recommendation of supplements as progressed cases can be quite sensitive to certain supplements. Side effects due to supplementation can occur through the die off of bacteria.

A full case history should be taken to properly establish which nutrients/supplements are important and therefore I highly recommend finding a functional medicine health coach or practitioner to work with you.

Gut healing

It’s important to address gut health and repopulate the microbiome, specifically as antibiotics are often an important first step in early Lyme management. Take a good quality multi-strain probiotic and repopulate via fermented foods such as sauerkraut.

Another important factor in gut health is food sensitivities. We don’t want to consume something which further increases inflammation and weakens your immune system. Your body has enough going on with Lyme disease, so eliminating these trigger foods – gluten, diary and other food sensitives is an imperative step.

Avoid stress and prioritize sleep

Mental stress and lack of sleep can make your immune system weaker. Hence, patients diagnosed with Lyme disease are advised to avoid mental stress and ensure they get undisturbed sleep. Around 8 hours of sleep would enable the immune cells to fight the infection more efficiently and help to restore health in a shorter duration.

Along with poor sleep, chronic stress can further dampen your immune system and exacerbate your symptoms. Find stress relief techniques that work for you – yoga, deep breathing, laughter, acupuncture, meditation!

Address toxicity & mould exposure

A common denominator that patients with Lyme disease have is heavy metal toxicity and mould toxicity.
Heavy metals make bacteria far more toxic. Or vice versa. The bacteria which thrive in heavy metal contaminated areas convert these heavy metals into a far more toxic components like dimethyl mercury or arsenic. These toxins are known to be super destructive and in sufficient quantity can lead very severe outcomes.

It is therefore important to detoxify heavy metals via high intensity PEMF combined with binders, sauna, hyperthermia, fibre rich diet, exercise, and so on. You can find more about PEMF and Detoxification here.
PEMF therapy is effective in heavy metal detoxification and also provides cells with the necessary energy to support the elimination.

Mould can result in an impaired detoxification, increased inflammation, damaged DNA/RNA, mitochondrial dysfunction and suppressed immune response. Mould can also reactivate old dormant viruses and flare up autoimmune diseases!

It is very hard to eliminate mould from the body. The only effective therapies are UBI, Ozone, Hyperthermia and good supplementation. Those with an elevated toxic body burden and suppressed immune system are significantly more susceptible to Lyme disease.
There is a mould detox box that is very effective at eliminating mycotoxins, please read the blog on mould here: Another excellent way to detox is coffee enemas.


Maintaining optimum physical activities is the key to faster recovery for patients with Lyme disease.

Light exercises such as walking could improve mood, boost immunity, and support joint health thereby minimizing the symptoms of this condition.


While antibiotics certainly have their place in the treatment of Lyme disease, they do not address the underlying root causes such as immune system dysregulation, inflammation, poor gut health, co-infections. The functional approach provides a safe, effective, and natural way to limit and address the manifestations of this infection and restore health.

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