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Biofilm: What It Is and How to Treat It

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Do you have patients with infections that subside for awhile but then reappear? Bacterial and fungal biofilms might be to blame. Read on to learn about biofilms and how to treat them.

Most Bacteria Are Present in Biofilms, Not as Single-Acting Cells

The popular image of bacteria depicts single cells floating around, releasing toxins and damaging the host. However, most bacteria do not exist in this planktonic form in the human body, but rather in sessile communities called biofilms. To form a biofilm, bacteria first adhere to a surface and then generate a polysaccharide matrix that also sequesters calcium, magnesium, iron, or whatever minerals are available.

Within a biofilm, one or more types of bacteria and/or fungi share nutrients and DNA and undergo changes to evade the immune system. Since it requires less oxygen and fewer nutrients and alters the pH at the core, the biofilm is a hostile community for most antibiotics. In addition, the biofilm forms a physical barrier that keeps most immune cells from detecting the pathogenic bacteria (1, 2).

The Current Model of Care Misses the Mark

The current model of care usually assumes acute infections caused by planktonic bacteria. However, since the vast majority of bacteria are hidden in biofilms, healthcare providers are treating most illnesses ineffectively. According to the NIH, more than 80 percent of human bacterial infections are associated with bacterial biofilm (3). While planktonic bacteria can become antibiotic resistant through gene mutations, a biofilm is often antibiotic resistant for many reasons—physical, chemical, and genetic. Treating illnesses associated with biofilms using antibiotics is an uphill battle. For example, in patients suffering from IBD, antibiotics appear initially to work, only to be followed by a “rebound,” where the symptoms again flare up, presumably due to bacteria evading the antibiotic within a biofilm (4).

According to the NIH, more than 80% of human bacterial infections are associated with biofilms.

Biofilms Are Hidden in the Nasal Passageways and GI Tract

Biofilms are well-known problems associated with endoscopic procedures, vascular grafts, medical implants, dental prosthetics, and severe dermal wounds. Biofilms found along the epithelial lining of the nasal passageways and GI tract are less understood.

The GI tract is an ideal environment for bacteria, fungi, and associated biofilms because of its huge surface area and constant influx of nutrients (4). For protection, the GI epithelium is lined with viscoelastic mucus, but it can be damaged in patients with excessive inflammation, IBD, and other conditions. This creates an opportunity for bacteria to attach to the surface and begin their biofilm construction. The epithelium to which it is attached is altered and often damaged (5, 6).

Biofilms Are Difficult to Diagnose

A number of problems make biofilms difficult to detect.

  • First, bacteria within the biofilm are tucked away in the matrix. Therefore, swabs and cultures often show up negative. Stool samples usually do not contain the biofilm bacteria, either.
  • Second, biofilm samples within the GI tract are difficult to obtain. The procedure would require an invasive endoscope and foreknowledge of where the biofilm is located. What’s more, no current procedure to remove biofilm from the lining of the GI tract exists.
  • Third, biofilm bacteria are not easily cultured. Therefore, even if you are able to obtain a sample, it may again test negative because of the microbes’ adapted lower nutrient requirements, rendering normal culture techniques null (7).
  • Fourth, biofilms might also play a role in the healthy gut, making it difficult to distinguish between pathogenic and healthy communities (4, 7).

Although a culture might come back negative, the microbes in a biofilm could still be pumping out toxins that cause illness. Some clinicians look for mycotoxins in the urine to identify biofilms (8), but I am not impressed by the research behind it yet. Because the bacteria sequester minerals from the host, mineral deficiency is probably associated with the presence of biofilms, although mineral deficiencies are all too common in the general population to use this alone as a diagnostic criterion.

Biofilms in the Background of Many Diseases

The medical community is increasingly dealing with antibacterial-resistant infections, with evidence of a biofilm at work behind the scenes:

  • Up to one-third of patients with strep throat, often caused by pyogenes, do not respond to antibiotics (9). In one study, all 99 strep throat-causing bacterial isolates formed biofilms (9).
  • Ten to 20 percent of people infected with Lyme disease, caused by burgdorferi, have prolonged symptoms, possibly due to antibiotic resistance and/or biofilm presence (10, 11).
  • Lupus flare-ups are induced by infection, inflammation, or trauma. In this autoimmune disease, cell death by NETosis instead of apoptosis turns the immune system against itself (12). Biofilms are suspected to be involved (13).
  • For chronic rhinosinusitis (CRS), “topical antibacterial or antifungal agents have shown no benefit over placebo in random controlled trials” (14). Bacterial and fungal biofilms are consistently found in these patients’ nasal passageways (14, 15).
  • Antibiotic treatment of irritable bowel disease (IBD) can work for a time, but flare-ups generally continue throughout a person’s life. Biofilms have been linked to both Crohn’s disease and ulcerative colitis (16, 17, 18).

Biofilms have also been implicated in chronic ear infections, chronic fatigue syndrome, multiple sclerosis, and acid reflux (4, 19, 20).

Is there a Link between Autism and Biofilms?

Peta Cohen, a pioneer in treating autism with a biomedical and nutritional approach, has found evidence of biofilms in autistic patients. When she disrupts the biofilm in these patients, she sees a huge “offload” of heavy metals in the urine and stool. Autistic individuals often have elevated mercury and lead levels (21). Bacteria aren’t choosy about which minerals they sequester during biofilm construction, and so Dr. Cohen’s explanation is that these patients also suffer from GI biofilms loaded with mercury and other heavy metals. Her experiences are as of yet only anecdotal; a PubMed search for “autism and biofilm” yields zero results. Check out my podcast here for what I believe are underlying causes of autism.

How to Treat Biofilms

Antibiotic after antibiotic for IBD. Corticosteroids for CRS. If a biofilm is at work, these standard “treatments” aren’t curing anything. Clinicians instead need to break down the biofilm, attack the pathogenic bacteria within, and mop up the leftover matrix, DNA, and minerals.

Biofilm disruptors are the first course of action. Enzymes such as nattokinase and lumbrokinase have been used extensively as coatings on implants to fight biofilms (22, 23). Cohen’s protocol recommends half a 50mg capsule of nattokinase and half of a 20mg capsule of lumbrokinase for small children with chronic strep throat and autism. Other promising enzymes include proteases, plasmin, and streptokinase (24).

Mucolytic enzyme N-acetylcysteine (NAC) is a precursor of glutathione and an antioxidant. Effective against biofilms on prosthetic devices, in vitro biofilms, and chronic respiratory infections (25, 26, 27, 28), NAC is recognized as a “powerful molecule” against biofilms (29).

Lauricidin (other forms: monolaurin, lauric acid, and glycerol monolaurate) is a natural surfactant found in coconut oil that helps inhibit the development of biofilms (30). In my practice, I also use it as an option for a gentler antimicrobial agent.

Colloidal silver is effective at treating topical biofilms, such as in wound dressings (31, 32). Applications in vivo are still under research. Although used successfully to treat a sheep model of bacterial sinusitis (33), colloidal silver did not show the same effectiveness in a small human trial (34, 35).

I recommend Klaire Labs InterFase Plus and Kirkman Biofilm Defense, two commercial products formulated to effectively disrupt biofilm.

Antimicrobial treatments follow biofilm disruptors. When necessary, I do use pharmaceutical antibiotics, but mixtures of herbal antimicrobials can be effective:

  • berberine
  • artemisinin
  • citrus seed extract
  • black walnut hulls
  • Artemisia herb
  • echinacea
  • goldenseal
  • gentian
  • fumitory
  • galbanum oil
  • oregano oil

Once the biofilm is destabilized and microbes are treated, binders help clean up the mess. EDTA disrupts biofilms and also chelates minerals in the matrix (36, 37). Chitosan and citrus pectin are two other options.

I can’t stress enough how important probiotics and prebiotics are in healing the gut and maintaining a healthy GI tract. Probiotics reduce pathogenic bacteria and have even been shown to disrupt the growth, adhesion, and activity of biofilms (38, 39). I recommend Primal Probiotics and Prebiogen or potato starch for prebiotics.

Hopefully the medical community will soon recognize biofilms as factors in many diseases and properly treat recalcitrant infections and illnesses.


  1. Does the EBV virus in particularly the virus that causes CAEBV have biofilms?
    If so what is a good enzyme to use for its treatment?
    I once was prescribed an enzyme that was harvested from the protective coating on earthworms (I know sounds really gross but when you are deathly sick I would take almost anything).
    I can’t remember the exact name of it but it was from the family of kinases. Do you know which one it might be?

  2. After I used biofilms disruptors irresponsibly (way too high doses) I developed a parasitic hyperinfection that i am now treating with medication. Now that my infection is stabilized, I need to try biofilms disruptors again, in appropriate doses, but I am concerned about my ability to expel the biofilms remnants. I would prefer not do regular enemas, as I am taking medication and do not want to lessen the concentration in my system. Are there recommended ways of flushing the biofilms toxins after they get disrupted?

  3. Does anyone have experience overlapping antibiotic with antifungal medications? There’s research out there that supports that the underlying mechanism to this combination therapy may be iron chelation.

    • I am taking both doxycycline and fluconazol. It does not appear to be disrupting biofilms. I still plan to add a disruptor supplement. ..Interesting about iron chelation though. I recently had to add an iron supplement due to a marked deficiency. I’m also vegan though, which can cause that.

  4. Hey Chris
    I am stocking up to start the antimicrobial for SIBO. Can you help my chose between Klaire and Kirkland for biofilm distruption? Also, Iberogast is great at helping me release trapped gas but it has never helped my motility. For the first time ever Senna isn’t even working on me. Lastly, my first run with Prescript Assist was SO painful. I want to stick with it this time to let it kill the bacteria. How long term does the die-off cause discomfort?

    My functional practitioner took your training and handed me your anti microbial protocol. She is an established physician, but new to Functional Medicine. I feel like I am her first ISBO case to treat. There were handouts and base advice but not enough experience to answer questions about variables and such. Thank you MUCH

  5. I am not a doctor. I am a patient suffering from Hidrenitist supurativa, rhumatoid cystic arthristist, they even did blood work to see if I have lupus. My inflamation is off the charts and even shows up in ctc scans. but rhuematoid numbers were not right for it to be that. They are sending me to a ruhematologist anyways.
    I seriously think I have a biofilm issue. My HS only heals after surgical removal of tissue and skin transplant. I think I have the kind that goes deep into the tissue bed because they keep telling me I have a healthy wound bed but no healing is occuring. Infact my wounds are spreading and when they inflame so do my joints.
    I have had fungus issues all my life. I have had dreams I am a fungus queen and mushrooms and moss grow wherever I walk.
    People who have HS said they only found certain diets to work but the other half say the diets are placebo and they notice no difference. I am all for placebos if they are making me feel better.
    I want to improve my diet but I do not agree with the diets people are doing. I think they actually make themselves allergic to foods they would never had any issues with if they had not made their bodies super sensitive to them making their living conditions even more of a nightmare. I would like to eat more foods that break up Biofilms… unfortunately if I was on one of their diets I think every single one of them is forbidden. Their poor bodies are complete hostages to their hosts.
    Please keep us informed. I know the knowledge is new but I do not think the situation is. I think its been around for a long time. I mean we know that the kids that survived the plague had silver spoons in their mouths after all.

  6. Dr. Kresser, do you have a particular regimen of the products recommended in this article that one should follow in disrupting & ridding themselves of biofilm? Thank you.

  7. Is there an Anti-Biofilm regimen you’ve designed of the products mentioned on this page? Thank you.

  8. My 30 yr. Old daughter has late stage Lyme and a huge biofilm, intestinal parasites. Hiw can she get rid of the biofilm?

  9. The best thing I have found for this is coffee enemas and mimosa Pudica by Microbe it does release bio film from the wall of the intestine. they also have binders to take after to absorb the toxins in the intestine.

  10. Do not take oregano oil. It is just as damaging as antibiotics. Dealing with the pain of just taking one capsule of it currently. You have been warned! If you want the benefits, include oregano (the herb itself) not the concentrated form (oil) in your diet. Good luck towards healing!!!