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Biofilms: The Invisible Threat Behind Chronic Infections


Unmasking biofilms and their role in chronic health issues, recurrent infections, and antibiotic resistance.

By: Dr. Coby L. Hanes, DC, IFMCP

Biofilms are responsible for many chronic or reoccurring infections. Biofilms interfere with detoxification and nutrient absorption, promote, and protect co-infections, create arteriosclerotic plaque, and give cancer cells a place to hide.

Biofilms can be a source of chronic inflammation, a well-known root cause of all chronic diseases.

Biofilms are responsible for a significant number of human infections and diseases, including chronic or recurring lung, bladder and sinus infections, wound infections, dental caries and periodontitis, endocarditis, and cardiac diseases. 

Medical devices and implants are especially prone to chronic biofilm infections including prosthetic joints, knee replacements, implants of any kind including breast implants, IUDs, pacemakers, surgical mesh, and catheters. The infections may not appear until years after the original surgery.

What Are biofilms?

Biofilms act as protective barriers for pathogens, allowing them to cloak and hide themselves to avoid detection by the immune system. They prevent the immune system from mounting an attack and can provide a barrier preventing medications like antibiotics from reaching the pathogenic organisms. 

Biofilms are a sticky layer of bacteria, yeast or fungi suspended in a thick matrix of proteins, polysaccharides (sugars) and lipids (fats). The sticky layer allows bacteria to bind to the lining of the lung, gut, urinary tract, or blood vessels where they can lead to chronic infection. 

If you’ve felt a film on your teeth, coughed up sticky phlegm or cleaned the gunk out from a stinky drainpipe, you’ve encountered biofilm. 

If you have an infection or illness that won’t go away, biofilms may be the culprit.


THE BIOFILM LIFE CYCLE: 1) Free-floating, or planktonic bacteria encounter a surface and become attached. They begin to produce slimy extracellular polymeric substances (EPS) and to colonize the surface. 2) EPS allows the emerging biofilm community to develop a complex, three-dimensional structure within hours. 3) Biofilms can spread via detachment of cells, or by “seeding dispersal.” Biofilm Montana State University

Biofilms & Reoccurring Infection

Microbes exist as both “planktonic” (floating) cells and “sessile” (attached) cells on surfaces. For generations, microbiologists have studied microbes in one way:  grown as single-species organisms on nutrient media. Today’s antibiotics were developed by testing their efficacy on the same single-species organisms grown on nutrient media in a lab.

The image of bacteria as a single species of organism floating around, releasing toxins, and damaging the host is woefully inaccurate. Many pathogens responsible for chronic infections do not exist in this single organism, free floating form in the human body. 

This misconception is based on an outdated model which is still tightly held by many in medicine. Sadly, this misconception leads to the continual prescribing of antibiotics, which might make patients feel better temporarily, but has little hope of irradicating the real problem. 

Why? Because bacteria, yeast, and fungi often attach to a variety of surfaces and form diverse communities which allows them to exhibit properties, behaviors and survival strategies that far exceed their capabilities as individuals.

Many pathogenic organisms form complex communities in biofilms. The biofilm allows them to attach to a surface and generate a thick matrix (think sticky phlegm), which forms a physical barrier, thus allowing the organisms to hide from the immune system, avoid antibiotics, and sequester nutrients along with numerous other complex survival mechanisms we’re just now beginning to understand.

In fact, sessile (attached) bacteria are 500–5000 times more tolerant towards antibiotics compared to their planktonic (single organism, free-floating) state. 

Additionally, microbial biofilms are naturally resistant to antibiotic doses up to 1,000 times greater than doses that kill single-species floating bacteria. 

Biofilms can occur anywhere there is moisture, nutrients and a surface for them to attach. This includes any body tissues, metals, plastics, and implanted medical materials or devices including catheters, IUDs, breast implants, surgical mesh, and pacemakers.

Common Biofilm Infections:

Biofilms are attributed to a number of chronic or reoccurring infections including chronic lung, sinus and urinary tract infections, chronic skin and gut infections, chronic Lyme disease, and are a major contributor to inflammatory bowel disease. 

  • H. pylori
  • Chronic Lyme disease and co-infections
  • Candida and other fungi
  • E. Coli and Cdifficile
  • Dental plaque or periodontitis
  • Chronic otitis media (middle ear infections)
  • Endocarditis or Pericarditis
  • Chronic wounds or skin infections, including MRSA
  • Many parasitic infections

In humans, biofilms are associated with 65% of all microbial infections, and 80% of all chronic infections according to National Institutes of Health.

Prosthetic and implantable devices are prone to contamination either immediately during surgery or anytime thereafter. 

Biofilms related to implanted medical devices: 

  • Breast Implants
  • Knee and other joint replacements
  • Catheters
  • Dental Implant
  • Contact lenses
  • Pacemakers and Prosthetic valves

Additionally, the risks associated with replacing an infected implant are high, and there is no guarantee that the bacteria will not return. It also takes a considerably lower bacterial load (≈10,000 times less) to infect a biomedical device, likely due to the lack of a blood supply, making implants much more prone to infection than your own tissues and organs. 

Khatoon, Z., McTiernan, C. D., Suuronen, E. J., Mah, T. F., & Alarcon, E. I. (2018). Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention. Heliyon4(12), e01067. Bacterial Biofilm on Implantable Devices 

Signs You May Have a Chronic Biofilm Infection

  • You have a parasitic, bacterial or yeast infection and a history of treatment resistance. 
  • You have chronic symptoms, yet no infections are identified on standard swabs or cultures. 
  • New infections show up after a round of antimicrobials. Suggesting the biofilm was sufficiently disrupted so that new organisms now show up on testing.
  • Previous treatments without a biofilm disruptor have not been successful.
  • If you have been sick for over one year or have an infection that you haven’t been able to clear.
  • If your symptoms improve with antibiotics, but they keep recurring. 

Biofilms Are Difficult To Diagnose

  • There are no standardized protocols for biofilm diagnosis in clinical practice.
  • Organisms within the biofilm are hidden in the matrix, so swabs and cultures often show up negative.
  • Biofilm samples within the GI tract are difficult to obtain, require an invasive endoscope and knowledge of where the biofilm is located.
  • Biofilm organisms are not easily cultured, so even if you are able to obtain a sample, it may test negative because of the microbes’ adapted lower nutrient requirements, thereby rendering culture techniques null.
  • Biofilms also play a role in the healthy gut, making it difficult to distinguish between pathogenic and healthy communities. 

Why Treatment Fails

To efficiently treat a problem, you must first fully understand the problem. Because medicine is still adhering to a model that assumes most infections are caused by a single bacterium and not part of a biofilm, the treatment is antibiotics, and if one does work try another and another. 

This is inefficient and ineffective care, because many bacteria are hidden in biofilms.

The continual prescribing of antibiotics does little to eradicate chronic infections. Additionally, these organisms are efficient at sharing gene mutations which encode for antibiotics resistance, meaning this practice creates more antibiotic resistant organisms. 

Mother nature is intelligent, and these organisms have developed very complex strategies for surviving. So, no matter if your doctor is using antibiotics or antimicrobial herbs, there must be a strategy to deal with the biofilm for either treatment to work. 

This is why patients suffering with chronic sinus infections, chronic Lyme, MRSA, or any other reoccurring bacterial or yeast infection often feel better while on antibiotics, however, a rebound of symptoms frequently follows.

Antibiotics also destroy our gut microbiome, a critical part of our immune defenses. 

Why Biofilms Make Treatment More Difficult

When pathogenic organisms hide themselves in a protective biofilm, treatment becomes more challenging. It makes it difficult to know exactly where the infection is, how much there is, and what antimicrobials the organisms might be susceptible to. 

This is true whether one is using antibiotics or antimicrobial botanicals. 

Biofilms provide a barrier against treatment, making it difficult to get any antimicrobial to the site needed.

Because of the thick biofilm and other sophisticated survival strategies, antibiotics often will not completely clear the infection, contributing to a “Rebound Effect,” and to the development of antibiotic resistance.

That is why recurrent infections including parasites, bacteria, yeast, or fungi such as Candida often require a biofilm disruptor in addition to antimicrobials. 

Biofilm Disruptors

Within biofilms, microorganisms can form diverse colonies and communicate with one another via cell signaling known as Quorum Sensing. Allowing these microorganisms to work together as an organized community, changing and adapting to their environment.

Therefore, to successfully eradicate chronic or reoccurring infections requires strategies to disrupt the biofilm and interfering with quorum sensing. 

Ways to eradicate biofilm

Since antibiotics rarely resolve these infections, one the most effective treatments of chronic infections is removal of the infected implant, device, tissue, or organ. [4] While that may seem radical, if it is a catheter, infected tooth, a breast implant, or other implanted medical device, it is the most expedient solution.

Next, clean up your diet, get off all sugar and refined carbohydrates, get plenty of quality sleep, hydration, and improve your gut health and immune function. Your body is amazing and can handle most insults and infections, provided it is not bogged down with a lack of sleep and an inflammatory diet.

Consider antibiotics or antimicrobial herbs, however, to be more successful combine them with a strategy to deal with biofilms. 

Whichever treatment you decide, keep in mind that the indiscriminate use of broad-spectrum antibiotics wreaks havoc on your gut microbiome (where 70-80% of your immunes system lives), which is your first line of defense against any infection. 

There is evidence that natural medicines have comprehensive inhibitory effect on biofilms. These natural therapies can disrupt the biofilm in your gut and alleviate symptoms, as well as make testing for specific bacteria easier.

Natural foods and supplements which can help to disrupt biofilms include Linoleic acid, (EGCG) from green tea, Honey & Propolis, Apple Cider Vinegar, Caprylic Acid, Stevia & Xylitol, Garlic, Ginger and Cranberry. 

Supplements include Ozone, NAC, Lactoferrin, EDTA, Zinc, Iron, Iodine, Monolaurin, Quercetin, Colloidal Silver, and Zeolite. Herbal Biofilm Disruptors include Andrographis, Turmeric/Curcumin, Berberine, Cinnamon, Black cumin, Oregano Oil, Neem and Eugenol found in Tulsi, clove, and cinnamon essential oil. 

My Top 3 Biofilm Strategies

There is no shortage of probiotics, essential oils, antimicrobial herbs and so-called biofilm disruptors. However, my clinical experience has shown the following natural solutions to be the most efficient and practical to chronic infections and biofilms.

The first thing is to set the optimal conditions for healing. This means healing the gut and optimizing the immune system by eliminating sugar, refined carbohydrates, and processed foods.

Optimal healing also requires a healthy liver and bile flow. For this I use specific whole food supplements from Standard Process, called A-F Betafood which contains organic beet root and other constituents which open the lymphatics of the liver, thins the bile and allows proper elimination of the toxins. This is critical because when these pathogenic organisms start to die off, they puke up all their garbage.

Throughout the process, adequate hydration is essential because, as I often tell my patients, “The solution to pollution is dilution.”

Once the optimal conditions for healing are set, I employ a 3-pronged approach to break up the biofilm and address the pathogenic organisms.

1. Antimicrobials – need to be specific to any known or suspected overgrowth. Different organisms require different botanicals, and knowing which botanicals to use with yeast, fungus, parasites, or bacteria is really where an experienced Functional Medicine practitioner becomes invaluable.

2. Enzymes – a combination of clinical grade enzymes including Serratiopeptidase, Proteases and Nattokinase which are proven to break up biofilm. Most practitioners have their favorites, and in my clinical experience Arthur Andrews Medical makes the best.

3. Bacteriophages – also called phages, are viruses that infect and replicate in bacterial cells. We think of most viruses as bad, however, these viruses are more like probiotics. They attach to pathogenic bacteria, inject their DNA and hijack the bacteria into creating more and more probiotic viruses until it breaks apart.

Phages are an advanced strategy in treating biofilm related infections. They can clear some biofilms, and are able to penetrate their way into biofilms by dissolving one bacterial layer at a time.

The word “bacteriophage” means “bacteria eater,” because bacteriophages disrupt bacterial metabolism and cause them to break apart.

Phages have been shown to resolve certain E. coli (Escherichia coli) and gram-negative infections. I have found them particularly useful for recurrent bladder, sinus, and some GI infections.

Stevia and Xylitol have also been shown to help break up biofilm in some chronic infections. For the sinuses, there is an over-the-counter product called Xlear with xylitol and grapefruit seed extract that works quite well when combined with other treatments.


Biofilm infections are a poorly understood part of chronic infections.  They make detecting infections challenging and make treatment using conventional methods almost impossible.

Often by the time I see some patients they have seen 4-6 other providers. They have done the typical elimination diets, have been tested and treated for SIBO, and they have spent a lot of time and money on supplements, testing and treatment.

The reason is that Every Patient is Unique, and there is no one size fits all. So, before you do any more internet searches, order any products or programs, or follow any health coaches, dieticians or friends that swear that the latest ______(fill in the blank) supplement, juice or essential oil saved their life, call us to make an appointment for a full Functional Medicine work-up.

Please, do not want to waste any more time, money, or sleepless nights suffering. You deserve better.

If you are looking for a clinically proven approach to overcome a chronic or reoccurring infection or digestive symptoms, click Consultation today.



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