Biofilms: Lyme Disease Gated Communities

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biofilms in a Lyme disease treatment image from Marty Ross MD

"I updated this Lyme disease biofilms article on December 13, 2017 to include new information about how biofilms form and grow; plus information about the herbal product Biocidin."  Marty Ross MD

Lyme disease biofilms are protective communities for Lyme germs. In these various forms of the Lyme bacteria hide from prescriptive antibiotics, herbal antimicrobials, and the immune system. In chronic Lyme and associated diseases they cause:

  • treatment resistance,
  • antibiotic resistance, and
  • relapse once antibiotics or herbal antimicrobials are stopped.

Biofilms are not unique to borrelia, the Lyme disease bacteria. They are known to occur based on scientific studies in various infections such as staph infections of the skin. In Lyme disease, Alan MacDonald MD has shown biofilms to exist in people with Lyme based on his microscopic exams of brain tissues.

About Lyme Disease Biofilms

In Lyme disease biofilms bacteria produce and cover themselves in a layer of slime composed of mucopolysaccharides. To add structure, the bacteria recruit a protein found in blood called fibrinogen. Then they convert to the protein fibrin. Because the fibrin gives structure, the bacteria in biofilms can rid themselves of their outer protein coverings. This makes it harder for the immune system to react against them. In addition the slime layer covers the germs so the immune system cannot see them. In addition antibiotics or antimicrobial supplements may have difficulty reaching the germs. In biofilms germs use efflux pumps to remove antibiotics creating antibiotic resistance.

Within the Lyme disease biofilms the germs establish highly organized structures and functions. For instance they have tubes they use to take in nutrients. They also communicate using various chemical messengers, excrete waste through channels and perform other complex activities to promote the longevity of the community. Biofilms require calcium and magnesium and contain other minerals and heavy metals.

Biofilms grow through a number of steps. First biofilms have to  stick to surfaces. Then germs in biofilms talk to each other through quorum sensing making the germs and biofilm stronger. Germs in biofilms use efflux pumps that flush antibiotics out. Biofilms also grow through germ swarming motility where some bacteria develop tails to rapidly spread.

Lyme Disease Biofilms and Treatment

In my practice I intentionally treat Lyme disease biofilms

  • at the end of treatment to prevent relapse or
  • when a treatment is not progressing well due to treatment resistance.

Some physicians address Lyme disease biofilms at the very beginning or throughout the entire course of a treatment. In my practice I do not do this. My observation is that 90% or more of my patients get well without specific biofilm treatments. We know based on the work of Alan MacDonald MD that biofilms exist in brain tissues of people with Lyme. However, there is no scientific evidence that they occur in every individual who has Lyme and associated diseases. Furthermore, even if they do exist in all that have borrelia infection, there is no scientific evidence that they universally block treatments.

One reason people can get better without specifically treating for Lyme disease biofilm is all antibiotics can decrease biofilm size. Research by Eva Sapi PhD shows that the antibiotics doxycycline, metronidazole, tinidazole, and amoxicillin can reduce biofilm size by various degrees. The best of these is the drug tinidazole which reduces biofilm by 50 to 55%. While doxycycline reduced biofilm by 40%, metronidazole by 30% and amoxicillin by 30%. Note she did not study the whole list of antibiotics I often use to treat Lyme disease described in A Lyme Disease Antibiotic Guide.

How to Treat Lyme Disease Biofilms

Based on my review of biofilm treatments in Lyme disease there are three scientifically supported approaches to eliminate biofilms and many theoretical treatment approaches.

Research-based Treatments

Eva Sapi PhD and her colleagues are performing groundbreaking Lyme Disease research.  In 2010 and 2011 she published two articles based on petri dish experiments in her lab. The first shows that the herbs otoba bark extract and cat's claw tinctures used together completely eliminate biofilm communities. They also  eradicate nearly every germ living in them. Another study of 5 different antibiotics shows that prescription tinidazole decreases the size of biofilm communities by 50 to 55%. It also eliminates the germs living in them by over 90 percent. Based on my review of her research, I believe the best antimicrobial approach that eliminates biofilms and the germs that live in them are the herbs otoba bark extract and cat's claw tinctures. Prescriptive tinidazole is a very close second though.

In late 2015 Dr. Sapi published another petri dish study showing that stevia extract from Nutramedix decreases biofilm size by nearly 40% while eliminating most Lyme germs in the biofilm. She also showed stevia can kill persister cells of Lyme. For more information about stevia see Stevia for Lyme Disease.

More recent studies show that Biocidin, which is a mix of various herbs, is a potent breaker of biofilms. Petri dish experiments show it eliminates nearly 100% of biofilm. It is proposed that Biocidin works in a number of different ways. One way is by preventing germs from sticking to surfaces; another is to block quorum sensing where germs in biofilms talk to each other making the germs and biofilm stronger. Germs in biofilms use efflux pumps that flush antibiotics out. And Biocidin appears to block these pumps. Finally it limits germ swarming motility where some bacteria develop tails to rapidly spread. Read more in Biocidin: A Potent Antimicrobial and Biofilm Breaker.

Theoretical Treatments

As I noted above biofilms require magnesium and calcium, have various minerals and heavy metals, and contain fibrin protein structures and mucopolysaccharides substances. Theoretical treatments address these various components. Some physicians treat biofilms by

  • starving the germs by eliminating or limiting calcium and magnesium,
  • removing minerals and heavy metals with the chelating agent EDTA, and
  • breaking up the protein fibrin matrix with enzymes like Lumbrokinase or nattokinase.

In theory, I understand these approaches. However, I think such approaches are overkill. Now I admit that I am a minimalist when it comes to treating Lyme and associated diseases. I believe that physicians should treat using as few supplements or prescriptions as possible to gain the maximum benefit. Even though I work with supplements, I do not think it is useful or appropriate for most patients to leave a medical office or a store with bags full of supplements. Regarding eliminating calcium and magnesium or limiting them, I do not support this. Biofilms exist in us, so of course they require the same minerals that we do to survive. I do not think we should starve the host (a person with Lyme) to kill the germ.

The only theoretical approach I use in my practice is the supplement Lumbrokinase. It breaks down the fibrin protein skeleton that holds the biofilm together. This alone is enough to break up the biofims. Using Lumbrokinase alone I have seen great improvements in my patients with treatment resistant Lyme and decreased episodes of relapse. An alternative to the Lumbrokinase is nattokinase, but it is a much weaker fibrin dissolving enzyme and I do not find it effective. Other enzymes like nattokinase and serrapaptase have been shown to effect biofilms in bacteria. However there are not studies that show enzymes work on Lyme biofilms.

Lyme Disease Biofilms Treatment Approach

Treat biofilms in the last four months of treatment to prevent relapse or anytime in treatment when resistance to antibiotics or herbal antimicrobials is blocking progress. As I noted above, most antibiotics can reduce Lyme disease biofilm size, so it is possible there is no need for the targeted treatments I discuss below.

So how do I design a treatment for biofilms? Currently I am using Biocidinas my favorite biofilm breaker.  Biocidin can be used with both herbal antibiotics and prescription antibiotics. My other favorite approach is to use otoba bark extract and cat's claw tinctures. When using these two herbs, I stop all prescriptive antibiotics. Dr. Sapi's work suggest this is the most effective approach, and this is what I observe in my practice as well. Another approach is to use prescriptive tinidazole in an antibiotic approach. I use lumbrokinase, if an antibiotic approach is working fairly well, or if otoba bark extract and cat's claw tinctures do not work, or if a person cannot tolerate the nausea or abdominal cramping that can occur with tinidazole. It is safe to add Lumbrokinase to any antibiotic regimen. As an alternative to lumbrokinase, I am adding stevia. I have only recently started using this herb and will report back within the next months about its real world effectiveness.

For information about dosing see the following separate articles I have on this site. For information about tinidazole see A Lyme Disease Antibiotic Guide. See also Otoba Bark Exract and Cat's Claw Tinctures, Lumbrokinase, and Stevia for Lyme Disease. For information about Biocidin see Biocidin: A Potent Antimicrobial & Biofilm Breaker.

One word of caution, when treating biofilms, sometimes Herxheimer die-off reactions can occur. In a die off reaction the immune system makes more inflammatory chemicals that can temporarily make the Lyme and associated diseases symptoms worse.


Sapi, E. et. al. Evaluation of in-vitro antibiotic susceptibility of different morphological forms of Borrelia burgdorferi. Infection and Drug Resistance 2011:4 97–113.

Sapi, E. et al. Effectiveness of Stevia Rebaudiana whole leaf extract against the various morphological forms of Borrelia Burgdorferi in Vitro. European Journal of Microbiology and Immunology 5 (2015) 4. pp. 268 -280. DOI 10.1556/1886.2015.00031

Humphreys, Corene. (2015) “Biocidin Research Update – The Science Behind the Success.” USA White Paper Webinar Series June 18, 2015. Retrieved from

Fresco, Rachel. (2014) “Biocidin: Clinical Protocols for Dysbiosis and Biofilms.” Retreived from

Gilbert, Leona. (2016) “Analysis of the Activity of Biocidin Compounds against Borrelia.” Unpublished presentation of research  conducted by Dr. Gilbert’s lab in Finland provided through personal communication from Rachel Fresco LAc PhD.

Marques, C.  “Activity of Biocidin against biofilms microbial biofilms.” Unpublished manuscript of research conducted by Dr. Marques provided through personal communication with Rachel Fresco LAc PhD.

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