Biofilm: How This Slimy Coating Is Causing Chronic Fatigue, Fibromyalgia, Irritable Bowel, and More!

Whether it is in our gut or on our teeth, bacteria survive and thrive in a structure that they create around themselves called biofilm.

Biofilm is just what the name implies: a sticky film made by living, microscopic critters. Why do they make it? To ensure their survival.

But there is more to biofilm than just that. It turns out that biofilm makes fighting an infection pretty tricky. Especially when this infection is lodged somewhere in the gut!  

The Slimy Goo That Ensures Microbial Survival

If you run your tongue along your teeth after a long day and feel a slimy coating, this stuff is the beginning of biofilm.

Little bugs, which are found everywhere inside and outside the body, create biological homes using a mixture of sugars and proteins.

These structures are pretty tough. For example, biofilm in the mouth is dental plaque. (1) You know – that hard stuff the dentist scrapes off your teeth with a special dental tool.

In a healthy gut that is filled with beneficial microflora, the biofilm that they create is thin mucus. This healthy biofilm allows the passage of nutrients through the intestinal wall. Healthy gut biofilm is moistening, lubricating, and anti-inflammatory.

The anti-inflammatory function of healthy biofilm is a big plus since these days, the gut is so prone to infection and inflammation from outside chemicals, drugs, and processed foods.

But what about an unhealthy gut biofilm? What is that like?

If you have an infection that just won’t go away, it could be due to unhealthy gut biofilm. Unhealthy gut biofilm will promote inflammation and protect bacteria, parasites, and yeast from even the strongest medications.  It does all the wrong things, such as:

  • Prevents the full absorption of nutrients across the intestinal wall.
  • Protects disease-causing microorganisms from the immune system.
  • Protects disease-causing microorganisms from antibiotics and antifungals (this means both herbal and pharmaceutical-grade).
  • Promotes inflammation.
  • Houses toxins like heavy metals.

The sturdy protection that biofilm provides from pathogenic bugs is one reason why some infections are so troublesome to resolve. Yeasts, parasites, and bacteria find shelter in the biofilm matrix, evading an onslaught of even the strongest of medications.

This applies to conditions like:

  • Chronic fatigue syndrome and fibromyalgia, which are often thought to have an infectious root.
  • Parasites.
  • Systemic Candida overgrowth.
  • Heartburn or GERD (gastroesophageal reflux).
  • Small intestine bacterial overgrowth (SIBO), which includes symptoms like heartburn, bloating, gas, abdominal cramping, brain fog, arthritis, acne, and other skin conditions.
  • Irritable bowel syndrome, ulcerative colitis, and Crohn’s disease. (2)

Unhealthy biofilm allows some infections to persist for years. This means that the body may become more susceptible to other infections, or co-infections, as well as other chronic degenerative diseases.

In short, unhealthy biofilms promote disease and accelerate aging.

How to Break Through Unhealthy Biofilm

Unhealthy gut biofilm is a hideout for many pathogenic, or disease-causing, microorganisms. This means yeasts like Candida. It also includes the more noxious varieties of bacteria that are related to things like diarrhea, constipation, weight gain, and bloating. (3) Parasites also seek refuge in a well-built biofilm.

Just like dental plaque that needs to be picked away at with a special dental tool, unhealthy gut biofilm is a slimy substance that adheres to the intestinal wall. And, as rigorous antibiotic therapy has shown, this slime is tough to break apart.

Unhealthy gut biofilm requires special care.

The goal of most antibiotic, antifungal, and anti-parasitic therapies is to get rid of the disease-causing microorganism. In the past, biofilms have made this near impossible. This was because we did not know about biofilms. Only recently have scientists discovered biofilms and their function in the body. (4)

First, Proteolytic enzymes can help to break apart the structure of unhealthy gut biofilm when taken on an empty stomach. Proteolytic enzymes are enzymes like protease, papain, and pepsidase FP. If you take these enzymes with food, they will only help with the digestion of food. Make sure the enzymes are high potency and in the right proportions, like Assist Full Spectrum Enzymes.

Some traditional herbal preparations break through tough biofilm. We now know that of anti-parasitic and antimicrobial herbs that are so effective because they naturally bust through and degrade biofilm. These are:

  • Clove, or Syzygium aromaticum
  • False black pepper, or Embelia ribes (5)

Apple cider vinegar, a popular all-purpose home remedy and household cleaning agent, is an acetic acid solution. Apple cider vinegar strips away important minerals from the biofilm matrix. It can be taken internally for this purpose. Start with two teaspoons mixed in 8 ounces of water.

Once you have restored the health of your gut, it is a good idea to promote the growth of a healthy biofilm to prevent a recurrence of an unhealthy biofilm.

There are two ways to do this – which anyone can do, and everyone should do.

1.    Eat a diet of whole and nutrient-dense foods. Eating this way sounds like a lot work, and it is. But your health matters. Think of it this way: if you only cut out all processed flours, sugars, and refined oils, you are off to a good start!

2.    Eat a diet rich in beneficial microbes. Fermented foods like sauerkraut, kimchee, and natto, cultured sauces and dips with sour cream and yogurt, and drinks such as probiotic beverages are all great sources of healthy bacteria.


What to Remember Most About This Article:

Biofilm is a sticky film created by microscopic bacteria to protect them and ensure survival. When unhealthy biofilm develops in the body, it makes it even more difficult to fight infection, especially an infection of the gut.

A healthy gut is filled with beneficial bacteria that create a thin biofilm that is anti-inflammatory and lubricating to the body. Unhealthy gut biofilm will prevent the absorption of nutrients, make pathogenic bacteria resistant to the immune system, and protect harmful bacteria from antifungals and antibiotics.

Unhealthy gut biofilm can be attacked with Proteolytic enzymes, antimicrobial herbs, and apple cider vinegar. Once health has been restored to the gut, you can promote a healthy biofilm by eating a diet rich in beneficial bacteria found in fermented foods and beverages! 


  1. A H Rogers. Molecular Oral Microbiology. Caister Academic Press. 2008. 65 – 108.
  2. S. Macfarlane, J.F. Dillon. Microbial biofilms in the human gastrointestinal tract. Journal of Applied Microbiology. 2007 May; 102 (5): 1187 – 1196.
  3. Peter J. Turnbaugh, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006 Dec; 444: 1027 – 1031.
  4. Sandra Macfarlane, et al. Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System. Appl Environ Microbiol. 2005 November; 71(11): 7483–7492.
  5. Vishnu Agarwal, et al. Prevention of Candida albicans biofilm by plant oils. Mycopathologia. 165 (1): 13 – 19.
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