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Dr. Ettinger’s Biofilm Protocol for Lyme and Gut Pathogens

Important Note:

In order to receive protocol information or help, you will need to become a distance patient – Distance Patient Application. I truly do want to help any and all who are interested, but it’s finally gotten to the point where too many people want free advice, treatment plans, personalized protocols…. I’m a firm believer in fair-exchange and I feel I have done that by providing the information in this post.

I will help you and I can create a tailor-made protocol for your individual situation. Please fill out the distance patient application (link above) or if you have questions about the program, please call me at 714-639-4360

Dr. Ettinger’s Biofilm Protocol for Lyme and Gut Pathogens

A specific question has been asked a lot lately, as to what is my protocol for busting through Biofilm.  Most of these questions have been directed to me by those diagnosed with or think they may have H. pylori bacterial infection or Lyme’s Disease (See also: Biofilms of Borrelia burgdorferi And Clinical Implications for Chronic borreliosis by Alan B. MacDonald, MD).  The reason that I’ve put this “biofilm busting protocol” post together is because of this fact: the day I discovered how to handle biofilm in the human body, was the day that chronic conditions, from the sinus to the prostate, were no longer a ‘project’, so to speck, to handle.  I hope this information is helpful to you.

First a little background on – what is biofilm:


Fig. 1: The biofilm life cycle. 1: individual cells populate the surface. 2: extracellular polymeric substance (EPS) is produced and attachment becomes irreversible. 3 & 4: biofilm architecture develops and matures. 5: single cells are released from the biofilm.  Related PostBiofilm Basics and Quorum Sensing and Biofilm

Here is an excerpt from a Klaire Labs, product monograph, which is a basic primer on the topic (My additions are in RED) The National Institutes of Health (NIH) estimates that 60% of all human infections and 80% of refractory infections (def. unresponsive to medical treatment) are attributable to biofilm colonies.  I have seen this, most commonly, in cases I’ve worked-up, where the pathogen is: Chlamydia pneumoniae, Pseudomonas aeruginosa, Helicobacter pylori, [Lyme disease - Borrelia burgdorferi] and Candida albicans.

  • The protection conferred upon microorganisms by biofilm allows them to achieve a high level of antibiotic resistance, stealth and invisibility.
  • Biofilm not only provide a physical barrier to antimicrobial agents (pharmaceutical antibiotics) and host antibodies, but facilitate the exchange of antibiotic-resistant genetic material between organisms and may contain antibiotic-degrading (hydrolysing) enzymes such as b-lactamase, effectively neutralizing incoming antibiotic (b-lactam antibiotics) molecules.
  • In fact, biofilm communities can be 1000 times more resistant to antibiotics than free-floating bacteria.
  • The decreased growth rate of sessile microorganisms (def. Permanently attached to a substrate; not free to move about; “an attached oyster”) also reduces their antibiotic susceptibility as most antimicrobial agents require rapid cell growth in order to effectively kill or inhibit the microbes.  Biofilm thus render pathogenic microorganisms enormously difficult to eradicate, and can almost single-handedly contribute to localized or systemic inflammatory reactions and delayed wound healing. “…. Once established, however, biofilm infections persist.  They are rarely resolved by host defense mechanisms, even in individuals with healthy innate and adaptive immune reactions.  Active host responses, such as invading neutrophils (the most abundant type of white blood cells in mammals and form an essential part of the innate immune system), can even be detrimental since those cells can cause collateral damage to neighboring healthy host tissue.  Biofilm infections respond only transiently to antibiotic therapy.” James Garth, PhD
  • Depending on the type of biofilm, one or more species of pathogens may be found embedded in the extracellular polymeric substance (def. Composed primarily of polysaccharides and can either stay attached to the cell’s outer surface, or be secreted into its growth medium).  Bacterial extracellular polymeric substance (EPS) maybe a carrier of, or may have heavy metals embedded in them, thus the indication for chelation w/EDTA. EDTA, ethylenediaminetetraacetic acid, is a chelating agent used to lower one’s body burden of heavy metals).

Pathogenic bacterial known to reside in biofilms include, but are not limited to: Borrelia burgdorferi (Lyme bacteria), Escherichia coli, Candida albicans (yeast and fungal mutation), Clostridium difficile (the most common cause of GI infection and a growing epidemic), Clostridium perfringens, Helicobacter pylori, Klebsiella pneumoniae, Legionella pneumophila, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, Staphylococcus aureus, Staphylococcus epidermidis, and Vibrio cholerae. Chlamydophila species such as Chlamydia pneumoniae don’t form biofilm, as they are intercellular, but may some how get accidentally get caught-up in them before entering a host cell. Here is a good video on Chlamydia and biofilm (Video [biofilm section 7:45 min. mark] – Dr. Wilmore Webley on C. pneumoniae & Biofilms).

The number of human diseases shown to be associated with biofilms is ever expanding and includes: chronic bacterial prostatitis, chronic rhinosinusitis (chronic sinus infections), cystic fibrosis pneumonia, infective endocarditis, periodontitis, recurrent otitis media, and virtually all device and implant related infections.  Strong evidence is also beginning to emerge for an etiologic (causative) role of pathogenic mucosal biofilm in gastrointestinal diseases, such as Irritable Bowel Disorders (IBS): Crohn’s disease and ulcerative colitis.

S. aureus biofilm

S. aureus biofilm

Dr. Marcus Ettinger’s Biofilm Protocol: You can get help with any of these steps by going to my Distance Patient Program/Application.

A. Biofilm Busting Products. This is just a partial list of the products that can be used, and not all of these products will be, or should be, used at the same time. Additional nutraceuticals may be needed, based on each individuals unique situation.

DO NOT SELF TREAT! Please read my updated, update below.

  1. Monolaurin or Lauricidin [AKA Glyceryl laurate or glycerol monolaurate] (monolaurin information).
  2. Nattokinase (a potent oral fibrinolytic enzyme supplement) Some prefer Boluoke Lumbrokinase.
  3. InterFase Plus™ (broad-spectrum enzyme formula w/EDTA)
  4. NAC (N-Acetyl-Cysteine)
  5. Lactoferrin (I like Nutricillin by Ecological Formulas) Dr. Anju Usman of Illinois states, “Our bodies make proteins, transferrin and lactoferrin, which mop up iron and block the ability of biofilm to form,” she said. “But pathogenic bacteria secrete iron chelators to snatch up iron and thus compete with the transferrin and lactoferrin for what they need to survive.”
  6. Xylitol (sugar alcohol)
  7. Nutiva Extra-Virgin Coconut Oil (42-52% Medium Chain Fatty Acids [MCFA], lauric acid, by volume)
  8. Serrapeptase (a potent oral fibrinolytic enzyme supplement)
  9. Guaifenesin
  10. Turmeric, Neem oil, Reishi Mushroom
  11. BFB-1™ & BFB-2™
  12. Smilax officinalis
  13. Carbonized Bamboo

IMPORTANT; PLEASE READ: Updated, Update – 19 August 2014 (Original: 08 Aug 2013): I have been helping patients with H. pylori, a biofilm producing bacteria, for almost 7 years now. In the beginning, eradicating this bug was very easy, in my opinion. As time progressed I noticed that the same protocol I had been using was becoming less and less effective – on first-timers, not re-treatments. There are now H. pylori strains that are now ‘multiple drug-resistant’. Medically there is no real explanation for this. Energetically there is a very good explanation, for me anyway, based on the research done by Rupert Sheldrake, PhD on Morphic Fields and Morphic Resonance. Please read about his theory for further clarification.

Because of this new shift in loss of effectiveness, in some patients, I have had to use more than one round of products or add more products to the protocol. The end result has always been eradication but it’s now taking more to achieve this result. Also, there are many people contacting me and letting me know that they have undergone triple and quadruple therapies to no avail. This proves in my mind that biofilm and the bacteria that create them are learning to defend themselves more effectively. They are adapting and mutating, genetically, to survive. Good for them and bad for us.

My theory is that with the introduction of hundreds of blogs, chat-rooms and websites devoted to H. pylori and biofilm, more and more people are self-treating. This self-treating is not killing the H. pylori or eliminating the biofilm but to the contrary, making them both stronger by building-up the biofilm defense. Every time a bacteria that produces a biofilm is unsuccessfully treated it becomes more resistant to the next protocol. When this is combined with the theory of Morphic Fields, it’s no wonder that H. pylori and biofilm eradication is becoming harder and harder to achieve. The point of all of this is that there is still effective treatment options available, it may just take a little more time and/or more products, allopathic (Prevpac or Pylera) and/or natural to get to the desired end result – H. pylori and biofilm eradication.

Lastly, I am not against self treating per se. The issue is that the information, out on the web, on biofilm and H.pylori is not comprehensive or clear enough for the layperson to be their own doctor or to successfully self-treat. I have always advocated and promoted that if you want to get better with or at something, you need a coach who is an expert in that field or subject. There are times and places where self-help is good , but biofilm and H. pylori treatment is not one of them. This is just my opinion.

Additional DataInterview with Dr. Cohen concerning biofilms and enzyme therapies (Nattokinase and Lumbrokinase) and Effect of xylitol on an in vitro model of oral biofilm (I have seen increased effectiveness since adding this to the protocol)

B. Avoid supplemental forms of minerals, especially: iron, magnesium and calcium during the biofilm protocol, as they may contribute to biofilm formation or increase biofilm density, thus decreasing the overall effectiveness of the biofilm protocol.

C. Take a broad-spectrum probiotic and prebiotic.  I like Now Foods brand Probiotic-10 or Biotics Research BioDof 7. VSL-3 can also be used (for a short period only) as well as Elaine Gotschall’s SCD™ yoghurt. These products will help to crowd out the bad bacteria, and also help disrupt and replace biofilm colonies along the mucus membrane.

D. Saccharomyces boulardii is another addition that will have positive benefits in any H. pylori, SIBO or Candida eradication protocol.

A recent meta-analysis involving 14 RCTs (1671 patients) evaluated the role of probiotics in H. pylori eradication [Tong et al. 2007]. In patients with H. pylori infection, probiotic supplementation improved eradication rates and reduced treatment-related side effects and individual symptoms [Tong et al. 2007]. In this meta-analysis, only one RCT evaluated S. boulardii and found that it decreased the risk of diarrhea when given concomitantly to patients receiving triple eradication therapy for H. pylori [Duman et al. 2005]. S. boulardii induces morphologic changes in H. pylori cells consistent with cellular damage [Vandenplas et al. 2009] and was shown to cause reduction in H. pylori colonization in infected children by 12% [Gotteland et al. 2005]. Of four RCTs testing S. boulardii in H. pylori infections, two were in children [Gotteland et al. 2005; Hurduc et al. 2009] and two in adults [Cindoruk et al. 2007; Cremonini et al. 2002]. Although there was no significant difference in H. pylori eradication between the S. boulardii and placebo groups, a significantly lower relative rate of AAD (16.1–25%) was observed. In a recent meta-analysis, the H. pylori eradication rate in the triple therapy group was 71% and increased significantly to 80% with S. boulardii supplementation [Szajewska et al. 2010]. Thus, S. boulardii may not be effective in eradicating H. pylori itself, but it is effective in reducing the side effects of the standard triple therapy (Prevpac).

E. Specific additions based on condition (This not a complete list):

  1. Candida albicansSF722* (10-Undecenoic Acid) Thorne Research.  This is as close as you can get to a medication and still be a natural substance.  There are a few chat rooms blasting this product, based on who knows what – can’t make everyone happy.  I’ve used SF722 for over 15 years and it is amazing – never a problem!  *Do not take SF722 if you are allergic to fishADP by Biotics Research is also a dynamite product. There are many other amazing products that can be added to complement the SF722 and ADP.  It’s really a matter of how many pills someone wants/doesn’t want to take per day or the severity of one’s condition, that will determine, if or which, additional products will be added.  If the Candida albicans overgrowth is severe, has not responded to holistic methods or has mutated into its more virulent hyphal form/fungal infection (nails, underarms, groin or skin); Diflucan (fluconazole), a prescription medication, is my personal preference, but Nizarol (ketoconazol) can also be used.  In Azole-resistant Candida albicans, lactoferrin must be added to either medication in order to increase their effectiveness.  There are certain B vitamins, minerals and amino acids that possesses synergistic properties and I find them indispensable when taking Diflucan (fluconazole), Nizarol (ketoconazole), and for supporting candida (yeast/fungal) treatment, and die-off symptoms.
  2. Chlamydia pneumonia, Klebsiella pneumoniae or Pseudomonas aeruginosa Pneumotrophin PMG by Standard Process, Inc. How it works.  I use this because it helps direct the body’s attention to the effected area and assists the body’s healing efforts to the lung, where it’s needed most.  Apex Energetics, H-PLR is also a mandatory addition. I also like to use OOrganik-15™ and Pneuma-Zyme™ by Biotics Research with some of my patients who manifest asthma, a chronic cough and/or emphysema like symptoms.
  3. H. pylori ProtocolHeartburn/gastritis/GERD or achlorhydria or H. pylori?
  4. Chronic bacterial prostatitis – Quercitin and Bromelain  combination by Now Foods. Decreases inflammation and oxidant stress in the prostate while increasing local concentrations of beta-endorphins.  Apex Energetics, H-PLR is also a mandatory addition.

E. Specific dietary restrictions and additions will need to be implemented.  These will determined on a case by case basis. After the desired result is achieved, there will need to be a rebuilding and regeneration protocol.  This is as important as eliminating the biofilm.


Biofilm testing is also available through Fry Laboratories. Fry Laboratories, L.L.C. is an independent clinical diagnostic and research laboratory located in Scottsdale, Arizona. We are committed to understanding chronic diseases and contributing to their cure through advancements in diagnostics and basic science research with emphasis on chronic inflammatory diseases, vector-borne diseases, and their intersection. Our clinical diagnostic laboratory offers general and targeted immunology services in conjunction with standard and cutting edge infectious disease detection and identification technologies. Our signature services include microscopy for visual identification and quantification of a wide range of blood-borne pathogens, co-infection serology, biofilm detection, and genus wide molecular detection technology with sequencing for individualized species and/or strain identification. We participate in both CAP and API quality control programs and provide worldwide testing service.

Diseases of Interest: Chronic Fatigue Syndrome, Fibromyalgia, Gulf War Veterans Illness, Chronic Lyme Disease, ALS (Lou Gehrig’s Disease), Parkinson’s Disease, Multiple Sclerosis, Autism, Lupus, Ulcerative Colitis, Scleroderma, Rheumatoid Arthritis, Osteoarthritis, Crohn’s Disease.

Infections of Interest: Borrelia (Lyme), Babesia, Bartonella, Anaplasma, Ehrlichia, Q-Fever (Coxiella), Toxoplasma, Rickettsia, Plasmodium, XMRV

Important: This post is not a substitute for medical advise or treatment and is for informational purposes only. Please consult with a physician before starting any nutritional or biofilm protocol on your own.

Additional data:

Effect of ciprofloxacin and N-acetylcysteine on bacterial adherence and biofilm formation on ureteral stent surfaces.

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112 Responses to “Dr. Ettinger’s Biofilm Protocol for Lyme and Gut Pathogens”

  1. Louise,

    I know this is may not be the answer you were looking for, but it’s the answer: Magnesium, Iron and Calcium can feed the biofilm by supplying it with some of the raw ingredients it needs to build-up its protective barrier. Take no supplemental minerals. Nattkinase or serrapeptase or lumbrokinse, along with lactoferrin might be helpful.

  2. Peter A. says:

    I’ve had trigeminal pain attacks for 8 years. At first, the family doctor thought it was a sinus issue. It took 5 years to find an ENT who correctly saw it as trigeminal related, he thought trigeminal neuralgia. He sent me to a neurologist who said my version was trigeminal autonomic cephalgia. From what I’ve read, “cluster headaches” sound closely related.

    The more I’ve gone back and forth with getting attacks and then using diet and sticking to a circadian-respecting schedule, and what seems to bring the attacks back, the more I think this is all about some kind of fungal or yeast infection/infestation in the sinus under the eye and probably also the whole eye or orbit or socket lining itself. I have a long list of reasons for thinking this.

    I hope you continue your work but the one thing I wonder about and worry about, is whether it is inevitable to only strengthen the little buggers more and more each time we knock back the colonies. Like using anti-bacterial soap only allows the strongest bacteria to survive and they grow back and thrive… You mention self-treating of H. pylori being involved in worsening the bug’s ability to fight treatment.

    I used to find olive leaf extract very effective, and pau d arco helpful. Now I’m not so sure they are working much anymore. What is maddening is it seems like there is some kind of balancing act where you have to accept their presence since they can never be totally killed off, and almost cultivate them like little unwelcome pets, yet not let them get out of hand. I’ve often found that when I am eating some of the yeast-causing foods but also taking most of the day to let them starve and using green juices and things like olive leaf, etc., somehow the attacks end. It feels like the bugs stay hidden if you don’t overfeed them, but if too much sugar or other such food too suddenly, they come out for a feeding frenzy and then the immune system goes nuts trying to clobber them, resulting in a painful trigeminal attack.
    just some thoughts

  3. Peter A. says:

    Thought I should add this:
    Over the 28 years I’ve been experimenting with “cleansing diets” and detox, the one and only reliable way to set back the yeasties seems to be FASTING, pure and simple. Meaning, no food, no calories of any kind, just water and rest, maybe some light exercise the first day but mostly just rest.

    The one thing that always mops up the herx die off is vitamin C but the problem is, as I see your site recommends not taking minerals because they might strengthen the biofilms, I have to buffer my C and find that the calcium and magnesium seem essential for sleep after knocking out a lot of the buggers. I normally take over 20 GRAMS of vitamin C a day, some of it as ascorbic acid powder buffered with potassium bicarbonate (from powder, but then later some buffered in the forms of calcium ascorbate and magnesium ascorbate. I don’t know how I would get through a few days even without ANY cal/mag/zinc/manganese/copper/selenium/chromium… geez, maybe that’s how I got all these biofilms in me!!!

    Seriously, I feel awful if I try to go without minerals for a few days… years ago I didn’t take them while fasting, but now I seem to be unable to do without vitamin C and minerals even during a fast.

  4. Robin Sole says:

    Hi – Upon reading your “about” page I see that you help other drs struggling to have a successful practice and as a person willing to mentor I am reaching out for advice. I was diagnosed with Multiple Sclerosis in 2012. I suspect I have lyme disease as well. I did get bitten by a tick in 2012. I do have 24 lesions on my brain. I have not worked since 2010. I have been treating my disease alternatively due to adverse reaction to interferon. I used to work in HRIS (Human Resources Information Systems) for Time Warner. I worked all the time in front of a computer. I did reduce EMFs to help with disease management. However, I need to earn a living to pay for my medical care. I am not on disability and I do not have family/husband to help me.

    I do not want to stop learning to heal my body. I read all the time. For example, I am trying Gerson Therapy now. However, I cannot go back to school as planned in 2010 because I have to pay dr bills. If I work in HRIS, they do not want me to have other career focus at night. How would you advise someone to transition in this type of situation? I have gotten better since 2010 (could not walk and removed amalgams than began walking). I am still with issues daily (spasticity on right side primarily) along with vision/hearing issues. I did IVs therapies (orthomolecular medicine) before I ran out of money. My IV dr was not into mentoring or educating me in anyway whatsoever.

    I would appreciate any advice you could give because right now, I just feel lost in a sea of information and a deep sense of knowing that doing what I used to do is not good for me. However, I do not have 150K and eight years to go to school. I am sick now!

    Robin Sole
    Cell: 919.605.5699 (from NYC in NC now)

  5. Peter, It’s mainly Iron that fortifies the biofilm. Yeast is also wrapped-up in the biofilm, so fasting alone may only give temporary relief.

    1. If it were me, I would take your minerals and Vitamin C with food 2. Potassium bicarbonate with Bragg’s Apple Cider Vinegar at night before bed. 2. Quercitin 800-1000mg’s with each meal along with some curcumin should help with reducing histamine and inflammation.

  6. maria jimenez says:

    I have pain all over my body I think I have fibromyalgia I been text for lyme one test was positive another negative and anther equivalent I don’t know if I have lyme or not. Please let me know what do you think. Thanks

  7. Courtney Hartman (@PK_Ultra) says:

    What do you recommend a person with Hidradenitis Suppurativa do?

  8. Courtney, possible benefits may come from following an alkaline diet (85% vegetables/fruits/nuts/seeds and 15% animal protein), alkaline minerals (potassium, magnesium, zinc), Juice vegetables (carrot, celery and cucumber) and vitamin D3. There are others but I would need to know more about you. If overweight or elevated blood sugar, lose weight! If you would like a personalized program, please call me at 714-639-4360 to find-out about my distance patient program or go here

  9. Maria, Get tested by Igenix Labs. They are the top Lyme lab in the country. In the meantime get on 1/day PQQ Energy by Now Foods.

  10. Robin, I can’t tell you what to do but if it was me I would be taking PQQ Energy by Now Foods with an additional 300mg’s of CoQ10 daily. Also, look into this –

  11. Hierge says:

    I’ve been a vegan for two years and am vectoring toward a raw vegan diet by the time I am 60. I’m full of Lyme now as well as my wife. We live in the woods and keep getting bit due to our indoor outdoor cats.

    I’m a little taken aback by the lack of discussion of carvacrol in terms of a primary frontal assault on biofilm. The sheer number of supplements and juggling of dosage etc on this blog give me a feeling that they are NOT working.

    I’m disregarding the rhetoric of long term Doxy on Lyme and am going on it for a year. I’m going to add probiotics daily at max dosage and adding sublingual carvacrol. In addition, I’m going to experiment with anti-biofilm products from Klaire labs to maximize the effect from Doxy.

    I don’t mean to insult anybody on this blog, but if you need all these supplements that indicates to me that you aren’t having success. Dr. Gabe Mirkin is the most honest doctor I’ve encountered on a national basis and he treats Lyme according to research. That’s the way I’m going now.

    We have chronic and recent Lyme. I’m experiencing numbness and arthritic symptoms. All recent since tick bite. I am not going to take ten different supplements. If I have too much inflammation then I’m defaulting to high doses of pharma fish oil per Dr. Sears.

    Convince me otherwise. I think this is the best protocol. If you can prove results that are superior without turning me and my wife in to lab rats then fine. We will preserve our lifestyle and live the best we can. I’m not going to be a slave to extreme protocols.


    Dave H.

  12. Dave,

    I’m not here to convince anyone, that is not the purpose of my blog. The purpose of my blog is to share what I have learned from treating patients for over 25+ years. When you have had the opportunity to treat hundreds… of Lyme and other biofilm forming conditions in patients, then I want to hear what has worked for you. I study biofilm, literally, on a daily basis, as I have that and other terms “Google alerted.” This means that whenever a new article is published on that topic I get it. I also communicate regularly with some of the top biofilm researches to share pearls as well.

    I looked into ‘carvacrol’ a long time ago. Carvacrol lacks the effectiveness to breakdown biofilm. Please read this: “…This inhibitory effect of carvacrol was observed at sub-lethal concentrations (<0.5 mM) where no effect was seen on total bacterial numbers, indicating that carvacrol's bactericidal effect was not causing the observed inhibition of biofilm formation. In contrast, carvacrol had (up to 8 mM) very little or no activity against existing biofilms of the bacteria described (Pseudomonas aeruginosa), showing that formation of the biofilm also confers protection against this compound."

    Note: Carvacrol was able to inhibit biofilm in less aggressive ‘biofilm-producing’ bacterial strains: Chromobacterium violaceum ATCC 12472, Salmonella enterica subsp. Typhimurium DT104, and Staphylococcus aureus 0074. Lyme is it’s co-infections are not weak bacteria.

    I sincerely wish you and your wife the best of luck with your Lyme treatments and the new diet. Please continue researching – the truth is out there.


    Dr. Ettinger

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