We Do Not Offer Testing Only Services

As the leading functional medicine clinic in the UK, we support our clients in optimising their health and tackling illnesses. To do this we offer tests that help us identify the root cause of their health concerns. With that in mind, our testing services are only for patients under consultation with our expert practitioners.

Find Out More About Functional Medicine I'm Still Interested Close
London Clinic of Nutrition
Google 4.7 220+

How is Lyme Disease Linked to Autoimmune Diseases?

Often with chronic Lyme Disease, where the infection has been present for more than 3 months, clients can also present with raised autoimmune disease markers.

How is Lyme Disease Linked to Autoimmune Diseases? Leaf


Lyme Disease is triggered by the Borrelia Burgdorferi bacteria, which can cause over 40 different symptoms including brain fog, muscle twitching, Bell’s Palsy, cognitive issues, neck pain and others

Lyme Disease is surrounded by misunderstanding and sometimes stigma because of the clinical challenges of symptom presentation, diagnosis and treatment. However, here at the Clinic, we specialise in using reliable Lyme Disease testing methods (such as a dark blood microscope) and have an excellent track record for supporting clients back to full health adopting a functional medicine approach.

Autoimmune Diseases, on the other hand, are conditions such as Hashimoto’s, Multiple Sclerosis and Rheumatoid Arthritis where the immune system gets ‘confused’ and starts attacking itself. Self-tissue in the nervous system, the thyroid, or the lining of the joints are often targeted and can be mistakenly attacked.

Often with chronic Lyme Disease, where the infection has been present for more than 3 months, clients can also present with raised autoimmune disease markers. Alternatively, Lyme Disease can trigger a remission of pre-existing autoimmune conditions such as Hashimoto’s.

This begs the question – how are the two connected?

Autoimmune Diseases and Bacterial Infections

Although a single cause for many autoimmune diseases is yet to be identified, research has suggested that bacterial infections – more specifically bacteria living in the gut – may be one of the triggers of such conditions.

Infections with bacteria such as H.Pilory have been linked to the onset of Rheumatoid Arthritis and a bacteria called Yersinia to the onset of Hashimoto’s. Klebsiella, another bacterial infection, has been linked to the onset of Ulcerative Colitis, an autoimmune condition where the colon and rectum can get severely inflamed.

One of the common mechanisms of how these bacteria can trigger ‘immune system confusion’ leading to autoimmunity is that the structure of some of these pathogenic bacteria mimics the structure of self-tissue – so ultimately the immune system cells go to attack the bacteria and sometimes start attacking the wrong self-tissue. This widely researched mechanism is called ‘molecular mimicry’.

The very same mechanism is also implicated in Lyme Disease, a bacterial infection, and autoimmunity onset. One of the major differences, however, is that Lyme Disease bacteria, the Borrelia, is much more complex than any other bacteria known to man.

Unlike most bacteria and very much like some viruses (e.g. Coronavirus), it has a number of projections on the cell surface called lipoproteins, over 120 of them, which can change depending on the purpose it is trying to achieve (such as hiding from immune system cells). This presents numerous opportunities for it to change its shape and confuse the immune system cells.

It is these cross-reactions to some of these proteins that trigger autoimmunity against the heart muscle, nervous system, and even parts of the brain.

Lyme Disease and Neurological Autoimmunity

Because of cross-reactivity with self-tissue, some of the nervous system cells can also be attacked. This can lead to symptoms such as brain fog, muscle twitching, numbness, balance issues, seizures and speech issues.

There is also another mechanism via which the Lyme Disease bacteria can trigger autoimmunity. It ultimately aims for the brain and often with chronic Lyme the bacteria cross the blood-brain barrier, triggering the immune systems of the brain ( the microglia) to launch a vicious attack against the bacteria. However, the self-tissue can often get caught in the crossfire meaning autoimmunity is possible. The microglia also supports important cells of the nervous system called Neurones, and when these are not helped by the microglia, this can lead to neuronal death – and unfortunately, neurons cannot re-generate by the brain.

Activation of microglial cells and neuronal death, potentially triggered by the Lyme Disease bacteria is linked to numerous neurodegenerative conditions such as Multiple Sclerosis, ALS, Parkinson’s and Alzheimer’s.

Therapies for Lyme Triggered Autoimmunity

As Lyme Disease can be much more than persistent a bacterial infection, it is important to test for and manage autoimmunity alongside it, via strategies such as:

  • Modulation of the immune system with herbs such as Astragalus, nutrients such as Vitamins A and D
  • Adopting an autoimmune Paleo style diet – aiming to exclude very inflammatory Gluten and Casein
  • Improve detoxification pathways – such as the liver detox pathways
  • Work on gut health with appropriate dietary interventions
  • Manage other bacterial and viral infections
  • Work on stress and underlying trauma

Our expert nutritionists and functional medicine practitioners can support your Lyme Disease with health testing alongside personalised nutrition and lifestyle recommendations to help you feel your best. Read some of our Lyme Disease testimonials here.


Daisy Ilchovska

Author Daisy Ilchovska

Daisy is MSc level educated and registered Nutritional Therapist, qualified Neuro Linguistic Programming Coach and a published Researcher in the area of Autoimmune Diseases. Her specialist areas of interest are Lyme Disease, Mould & Other Environmental Illnesses such as Heavy Metal Toxicity, MCAS, Autoimmune Diseases, Brain Health, Neurodegenerative Diseases, Hormonal Health, Fertility and Gut Health.



Sign up to receive free recipes, health tips and more