Chronic Inflammation and Infections
Cesar Collado
April 6, 2020

An Explanation of Biofilms

By Cesar Collado

Science and Medicine are often misunderstood by the chronically ill.  Given the complex nature of medicine, explanations on why we are sick are few and seldom grasped by the patient who follows treatment direction.  When it comes to inflammation and infection, it is also common that a physician may not have a clear answer when explaining diagnoses and treatment. 

What is Biofilm? This article is intended to explain what biofilms are and, in simple terms, why some chronic infections and inflammation are “chronic” and difficult to treat permanently.  While current medical understanding has a clear understanding of bacterial and fungal infections, relatively little research has been published on the detection and treatment to remove biofilm. The National Institutes of Health (NIH) revealed that among all microbial and chronic infections, 65% of all infections, and 80% of chronic infections, are associated with biofilm formation.  

What is Biofilm?

Infections and inflammation are rarely caused by a single microorganism in the body.  In fact, microorganisms of different species (bacteria, fungi) can clump together to form a functional matrix called biofilm.  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 resistant to most antibiotics and antifungals. In addition, the biofilm forms a physical barrier that keeps most immune cells from detecting the pathogenic bacteria. 

Chronic infections from fungi commonly occur in Chronic Rhinosinusitis (“CRS”) and in the gut, where 80% of the immune system exists as well as the body’s microbiome.  The microbiome is composed of trillions of bacteria, fungi, and viruses.  Both sinus and intestinal passages have a mucosal lining that both keep the pathogen from entering the blood system, but also serve as a medium for inflammation and infection. In fact, mucous production can provide nutrients for the microorganism to reproduce. 

Non-Medical Examples of Biofilm

To put this in perspective, here are two better understood examples of biofilm.  Both pond scum and the dark, slimy gunk that can accumulate in our dirty or clogged water drains as well as faucets at home (inside and out) are examples of biofilm.  To clean pipes, it sometimes requires pumping detergent with a high PH (10+) with hot water (115 degrees F) to clear pipes.

Another example of biofilm is the clear film that develops on our teeth and that we can feel with our tongues. Simply put, our mouths house bacteria.  Biofilm feeds on the food we eat.  It especially forms when we eat sugars or carbohydrates.  Once biofilm is removed, it grows back quickly, usually within 24 hours.  This is why we brush our teeth twice a day with a mild detergent (toothpaste) to remove the biofilm which will eventually turn into plaque. 

Biofilms in Chronic Rhino-Sinusitis

When Microorganisms (bacteria & fungi) enter the sinuses, the immune system reacts to the pathogen by deploying eosinophils. The immune system immediately releases eosinophils at levels far exceeding those needed to remove the microorganism. This increased inflammation results in damage to the sinus tissue lining. When a rupture occurs, damage to the smooth lining creates cavities in the sinus, where common bacteria (such as Staphylococcus aureus, locally found on the skin, hair, and in the nose) binds to the mucosal pits. With continuous inhalation and over time, additional Staphylococcus bacteria bind to form a protective matrix around bacteria, called biofilm. This matrix attracts additional bacteria and fungi.

Treatment can include antibiotics, twice a day nasal rinsing with a nasal rinse system and an antimicrobial dietary supplement such as AgrumaxAgrumax Dietary Supplement a concentrated citrus seed extract that can be added to a nasal rinse.   Surgery is sometimes required to effectively, physically fix the passages and irrigate to remove biofilms.

Biofilm in Wounds

A chronic wound is a wound that is stuck in the inflammatory phase of healing and cannot progress. Over 90% of chronic wounds contain bacteria and fungi living within a biofilm construct.  Each biofilm aggregation of microbes creates a distinct biofilm with differing characteristics so that any treatment approach has to be tailored to the specific biofilm. Defining the characteristics of that biofilm and then designing a therapeutic option particular to that biofilm is currently challenging and evolving in practice.

Antibiotics alone do not suffice.  Biofilm becomes resistant to antibiotics 48–96 h after formation. Identifying the multiple bacteria and fungi that make up a specific biofilm using polymerase chain reaction (PCR) allows directed therapeutic maneuvers such as application of specific topical antibiotics and biocides to increase the effectiveness of the debridement.

By repeatedly treating the wound on a regular schedule, the biofilm is forced to reattach and reform, during which time it is susceptible to antibiotics and the body’s host defenses. Identifying the multiple bacteria and fungi that make up a specific biofilm using polymerase chain reaction (PCR) allows directed therapeutic maneuvers such as application of specific topical antibiotics and biocides to increase the effectiveness of the debridement.

Biofilm in the Gut

The presence of bacteria and fungal biofilms appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut. The gut houses the immune system as well as the microbiome.  The gut microbiome is composed of trillions of microbes (bacteria, fungi, viruses and other microorganisms) that populate the microbiome.  Some are “good” microbes while others are not.  The “good” microbes aid in maintaining a balance between the two. When the balance is not maintained, an overgrowth of “bad” microbes can occur, resulting in inflammation or a leaky gut.  The gut microbiome plays a very important role in your health by helping control digestion and benefiting your immune system and many other aspects of health. An imbalance of unhealthy and healthy microbes in the intestines may contribute to inflammation, infection, weight gain, high blood sugar, high cholesterol, and other disorders.

In contrast to oral biofilms, the occurrence and features of healthy gastrointestinal mucosal biofilms, are poorly understood. This pertains to the difficulty in sampling the gastrointestinal tract of healthy persons. Biofilms in the intestines can become a source of imbalance that can result in chronic gut issues.

Inflammatory bowel disease (IBD) symbolizes a group of intestinal disorders in which prolonged inflammation occur in the digestive tract (esophagus, large intestine, small intestine mouth, stomach). Both genetic and environmental factors (infections, stress, diet) are involved in the development of IBD. As we know that bacteria are found in the intestinal mucosa of humans, clinical observations revealed bacterial biofilms are often associated with patients of IBD. Various factors and microbes are found to play an essential role in biofilm formation and mucosal colonization during IBD. 

A common problem associated with diet and antibiotic use is candida overgrowth.  Candida Albicans are single cell yeasts found in the microbiome.  A person’s diet has profound impact on Candida overgrowth.  Sugars, simple carbohydrates, and process foods are “favorite” nutrients for Candida.  Candida species are known for their ability to cause superficial and systemic infections in people. One specific feature of Candida species pathogenicity is their ability to form biofilms, which protects them from external factors such as host immune system defenses and antifungal drugs.

Gut issues caused by inflammation can result in IBD and autoimmune disease and should be addressed by a physician. Endoscopic examination is often required to provide a visual assessment for the physician.  Treatment often includes an antifungal diet, oral antifungal medications, and ingesting a natural antimicrobial dietary supplement to help maintain the balance in the microbiome and  inhibit candida overgrowth.  Mixing drops of the dietary supplement, Agrumax in water consumed daily can help maintain that balance.

Taking probiotics and prebiotics is also essential in maintaining a healthy gut. CitriSafe Eater’s Digest Prebiotic/Probiotic is particularly effective when dealing with Candida overgrowth.  The specific probiotic strain (Saccharomyces boulardii) has been shown to detoxify mycotoxins due to surface binding to the yeast cell wall. In combination with the FOS prebiotic, a product is created that promotes the production of beneficial bacteria while preventing the production of pathogenic bacteria and yeast. Additionally, this probiotic does not colonize the gut. 

Physical removal of Biofilm (Emptying the Bowels)

Colon cleanses have been used since ancient times; however, there is limited medical literature published to date of the benefits.  It is most often employed by functional and integrative medicine physicians. The concept is that clearing out the bowels removes unnecessary waste, toxins, and biofilms.  There is evidence that the laxatives used to clear the bowels prior to a colonoscopy provides patients with many detectable improvements in bodily function, including neurological.  Symptoms like fatigue, joint pain, bloating, and skin irritation are cited to be alleviated. There is also a connection of bowel health to colon cancer.

3 Methods to Emptying the Bowels  

  1. The first is to have a healthcare professional irrigate the bowels.  In this situation, a professional will irrigate the colon with gallons of water.  This method is indicated when normal laxatives are not working for an individual prior to a colonoscopy where a cleared out bowel is essential.
  2. Some people will use  a laxative normally used pre-colonoscopy like Magnesium Citrate or PEG, which are sold over the counter with specific directions that can accomplish the cleanse.  Sometimes evidence of blood or black residue provides guidance to see a physician.  Caution must be taken to address some of the risks of dehydration and electrolyte imbalance that come with utilization of a laxative in larger doses.
  3. Maintaining a healthy colon is also highly recommended.  Fortifying your diet with healthy foods is the preferred method.  This includes consuming:
    1. Plenty of water
    2. Fruit and vegetable juices
    3. Diet rich in fiber
    4. Fermented foods
    5. Resistant Starches 
    6. Complex Carbohydrates
    7. Lemon juice 
    8. Some herbal teas


The recognition of Biofilm formation in the body is important when seeking medical treatment for inflammation and infection.  As mentioned earlier, chronic conditions will often be treated with a single medication that alleviates the symptoms only to return. Chronic sinusitis and gut issues often require more than just medication.  They require a process to break down and remove biofilm, if that is the issue. Some dietary changes and dietary supplements can become essential maintenance to eliminate the chronic element of your illness. This may be an important discussion to have with your physician.

If you would like to share your story, please comment on this article.

About the Author:  

Cesar Collado is a former pharmaceutical R&D senior executive, venture capitalist, and seasoned strategy consultant in biotechnology and technology industries in general. He currently works as an advisor to multiple technology start-ups and advises several companies with technology solutions, including companies that provide healthcare and other services for environmental illness.

Cesar worked with MicroBalance Health Products from 2014-2019, where he had responsibility for strategy, revenues, marketing, and finance, as well as, writing all original content for the company’s newsletters during his tenure. Cesar is passionate about awareness and treatment of environmental illness as a significant, unmet and misdiagnosed, medical need. He has partnered with Integrative Physicians, Bau-Biologists, Environmental Inspectors, Mold Remediators, HVAC IAQ Specialists, and other professionals to generate educational materials for the environmentally ill. Cesar currently writes original content for ImmunoLytics, Bio-Balance, and CitriSafe: Protocols and Products for a Healthy Life. 

  1. Vidyasagar, Aparna.  “What are Biofilms?.” LiveScience. December 22, 2016.
  2. Regulski, Matthew  “ Biofilm-hijacked inflammation: the missing link to hard to heal wounds.” Wound Management and Prevention. April 2019.
  3. Attinger, Christopher, et. al. “Clinically addressing Biofilm in Wounds”. Advances in Wound Care. June 2012.
  4. Kernien, John et. al. “The Interface between Fungal Biofilms and Innate Immunity” Frontiers in Immunology. January 10, 2018
  5. Collado, Cesar. “Bacterial and Fungal Biofilms in Chronic Sinusitis and Antibiotics Resistance. Treatment and Prevention of Recurring Fungal Sinusitis and Mold-Related Illness” Sinusitis Wellness. April 15, 2019.  Copyright Reg. TXu 2-179-218
  6. Tytgat, Hanne, et. al. “Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?” Trends in Microbiology. September 12, 2018.
  7. Cavalheiro, Mafalda, et. al.  “Candida Biofilms: Threats, Challenges, and Promising Strategies”. Frontiers in Medicine. February 13, 2018


  1. Steve Popovich

    Good overview.

  2. Wendy Clark

    Excellent information! This is written and worded perfectly so that it is easy to understand, even for those who are not in the medical field. Thank you for publishing such valuable information. I have suffered from the symptoms of biofilm for far too long and the information in this article was extremely helpful and has given me renewed hope!!


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