What are Biofilms?

If you’ve ever dealt with symptoms that seemingly improve, only to come back again, you are not alone.

That cycle can be frustrating, discouraging, and confusing. It’s difficult to understand why it’s happening, especially when you have followed the plan, taken the supplements, or completed the course of treatment exactly as recommended. 

In many cases, this pattern isn’t a sign that treatment failed or that you did something wrong. It’s a clue.

That waxing and waning pattern is one of the most common clues clinicians see when biofilms are involved.

Understanding biofilms, how they affect treatment, and how they’re addressed can help make treatment more effective and longer-lasting.

What are Biofilms? 

Bacteria, yeast, and other organisms live all around us and inside our bodies. Most of the time, we rarely ever notice them.

These organisms do not always exist on their own. Instead, they attach to a surface and build a sticky, protective coating around themselves. You can think of this coating as a fence. It shields the microbes inside and helps them survive conditions and treatments that would normally eliminate them.

That protective coating is called a biofilm.

Inside a biofilm, microbes don’t act alone. They function as a coordinated community that can include bacteria, yeast, protozoa, fungi, and archaea. Living this way allows them to share resources, communicate, and protect themselves more effectively.

Biofilms tend to form in stages: Microbes will first attach to a surface. More organisms join, and the protective layer begins to build. Over time, the biofilm matures into a stable structure. Later, during the dispersal phase, some microbes can break away from the group and go on to form new biofilms elsewhere.

Once microbes are nestled and living inside a biofilm, they behave differently than they do on their own. Studies show that microbes in biofilms are often far more resistant to antibiotics and antimicrobial treatments. In some cases, the dosage required to affect microbes in a biofilm compared to the same organisms in a free-floating state can be 10 to 1,000 times higher 1 2.

Biofilms can also interact with the immune system in ways that promote ongoing inflammation and interfere with normal healing, as noted in a 2023 review 3.

Biofilms themselves aren’t inherently harmful. They’re a normal microbial survival strategy. Problems arise when pathogenic or imbalanced microbes dominate these communities, or when biofilms contribute to persistent inflammation and symptoms that don’t fully resolve.

A Familiar Biofilm Example

One of the easiest ways to understand biofilms is to look at a commonly occurring situation for many people: dental plaque.

Bacteria in the mouth adhere to the surface of the tooth and form a visible, sticky layer. As that biofilm matures, it produces acids and enzymes that can damage tooth enamel and irritate the surrounding gums. Over time, this triggers inflammation, which can lead to gingivitis (gum inflammation) if the biofilm is not removed 3.

Dental plaque is a useful example because it shows how biofilms work in plain sight. The microbes are not just present. They are organized, protected, and actively interacting with the surrounding environment. Now you can somewhat imagine the same basic process occurring anywhere else in the body, even if it’s not always visible.

Where Do Biofilms Live?

While dental plaque is a familiar example, it is certainly not the only place biofilms can form.

Biofilms have been identified in many less visible areas throughout the body. Anywhere microbes regularly interact with tissues and can persist despite treatment efforts, biofilm formation becomes possible.

Biofilms have been identified in:

• The gastrointestinal tract 4 
• Blood vessels 5
• Nervous system 6 7
• Urogenital tract 8 9
• Skin 4 
• Ear canal 4 
• Respiratory tract 4 

Why Biofilms Matter to Gut Health 

Biofilms matter in gut health because they help explain persistence.

Gut conditions like irritable bowel syndrome (IBS), irritable bowel disease (IBD), and small intestinal bacterial overgrowth (SIBO) are often characterized by symptoms that linger, fluctuate, or return after treatment. In these cases, microbes may not just be present—they may be protected, organized, and working together in ways that make them harder to fully resolve.

Research supports this connection. In a 2021 study comparing patients with IBS or IBD to healthy controls, biofilms were found far more frequently in those with digestive disease 10. Biofilms were present in 57% of patients with IBS and 34% of those with ulcerative colitis, compared with just 6% of healthy controls. Their presence was also associated with more diarrhea and higher markers of gut inflammation.

In other words, biofilms were not just present. They often appeared alongside more severe and persistent digestive disruption.

This raised an important question for us. If biofilms are helping microbes persist in the gut, could they also be contributing to conditions like SIBO, where treatment resistance and relapse are common?

That question led us to examine this more closely in the clinic.

We examined what happened when a biofilm disruptor was added to an herbal antimicrobial protocol for SIBO and intestinal methanogen (IMO) overgrowth. What we found was encouraging. Patients who included a biofilm disruptor experienced significantly greater reductions in hydrogen and methane gas levels compared with those using herbal antimicrobials alone. 

Because breath gas levels are one of the primary ways SIBO and IMO are measured, larger reductions suggest treatments may be reaching microbes that would otherwise remain protected.

For people who have struggled to fully resolve SIBO, or who see progress stall or reverse, this research highlights a meaningful and actionable missing piece.

Signs of Biofilm 

Biofilms aren’t something you can confirm with a single lab test. Instead, clinicians consider biofilms when certain patterns keep showing up.

That said, there are certain situations where clinicians may start to consider biofilms as part of the symptomatic picture 10 11: 

• Symptoms that improve temporarily with treatment, then return once treatment stops
• Partial responses to antibiotics, herbal antimicrobials, or antifungals
• Repeated treatment courses that seem to lose effectiveness over time
• Ongoing inflammation despite thoughtful dietary habits and gut support
• Strong die-off reactions that do not translate into lasting improvement

These signs aren’t diagnostic on their own, but they help explain why progress can stall or unravel.

Biofilm Treatments

Because biofilms can make microbes harder to reach, clinicians often consider them when standard treatments don’t work as expected or only help temporarily.

Some approaches that have been studied or used clinically include:

• Probiotics, which research suggests may help prevent the development and spread of pathogenic biofilms 12 
• Herbal antimicrobials, including compounds such as oregano, cinnamon bark, and clove bud, which have shown biofilm-disrupting activity in laboratory studies 13
• Enzymes, which are designed to help break down components of the biofilm structure, including polysaccharides, proteins, and fibrin-like material 14

In our recently published study, the biofilm disruptor used was Biota-Dissolve, and the herbal antimicrobial was our Biota-Clear line.

In some cases, medications may also be used, depending on the situation. These can include antibiotics, antifungals, antiparasitics, or antimalarials, such as doxycycline, metronidazole, amoxicillin, nystatin, amphotericin B, ivermectin, albendazole, or hydroxychloroquine 15 16. 

Biofilm FAQs

Are biofilms good or bad?

Biofilms themselves aren’t inherently bad. They’re a normal microbial survival strategy and exist throughout nature, including in and on the human body.

Biofilms become clinically relevant when they’re dominated by pathogenic or imbalanced microbes, or when they contribute to persistent inflammation, symptoms, or treatment resistance. In those situations, biofilms can help explain why symptoms linger or keep returning.

Do biofilms mean I have a chronic infection?

Not automatically.

Biofilms can be present without causing symptoms, and their detection does not automatically mean there is an active or harmful infection. They are one factor clinicians may consider when symptoms are persistent or difficult to resolve, but they are not a diagnosis on their own.

Can biofilms be tested for?

Direct testing for biofilms is limited and not routinely available in clinical practice.

In most cases, biofilms are inferred based on patterns, symptoms, and response to treatment rather than identified through a single lab test.

Can biofilms cause die-off symptoms?

They can.

When microbes are disrupted, whether through antimicrobials, antifungals, or biofilm-focused strategies, some people experience temporary symptoms such as fatigue, brain fog, digestive changes, or flu-like feelings. These reactions are often referred to as die-off.

Not everyone experiences die-off, and stronger reactions don’t automatically mean treatment is working better. These symptoms usually reflect how the body is responding to microbial shifts and inflammation, rather than serving as a measure of success.

For this reason, die-off symptoms are best interpreted in context and managed strategically, rather than used as a signal to push treatment harder.

Bottom Line

Biofilms are not something most people have heard of, but they help explain patterns many people recognize: symptoms that linger, treatments that help but do not fully resolve the issue, or progress that feels fragile or incomplete.

Understanding biofilms helps explain why some gut symptoms persist and why treatment can stall or relapse.

This is an evolving area of research, and one we are actively studying in the clinic. Our recent work exploring the role of biofilms in conditions like SIBO reflects a broader commitment to looking beyond surface-level explanations and identifying why some cases are more persistent than others.

If your gut symptoms keep returning or never fully resolve, working with a clinician who understands biofilms and complex gut conditions can be a turning point.

Our team at The Ruscio Clinic specializes in evidence-informed, individualized care for gut health and related conditions. If you would like personalized guidance, we invite you to learn more about working with our clinic.

Dr. Michael Ruscio is a DC, natural health provider, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.