The Hidden Role of Biofilms in Gut Health and Dysbiosis
If you’ve been stuck in a cycle of gut issues that won’t resolve—whether it’s IBS, SIBO, or IBD—biofilms could be why. These sticky, protective layers allow bacteria and other microbes to hide from treatment, disrupt digestion, and keep your gut in a constant state of irritation.
Most gut protocols miss this entirely. They focus on killing bacteria without addressing the biofilm itself. And if you go in too aggressively? You risk damaging the gut lining or wiping out beneficial biofilms that actually support your health.
The key isn’t to “bust” all biofilms—it’s to remove the harmful ones while protecting the beneficial ones that keep your gut balanced.
In this article, I’ll walk you through what biofilms are, how they impact digestion, and the research-backed strategies that actually work. No gimmicks, no extremes—just a smarter way to finally get your gut health back on track.
What Are Gut Biofilms? A Simple Explanation
When we think of the microorganisms in our guts, we tend to think of them as free-floating organisms. Though some organisms exist in isolation (planktonic microorganisms), most live in complex communities (biofilms).
Biofilms are essentially fortresses that microbes create so that they can be protected and hide from the immune system. These fortresses are very large and often host many diverse microbial species. These include bacteria, yeast, archaea, and even parasites.
In actuality, biofilms look very similar to mucus. They are green to yellow in color and are stuck like a plaque to the inside of the intestines. They are made out of a specialized goo that is secreted by certain microbes. The scientific name for this goo is “extracellular polymeric substances (EPS).”
Though biofilms can make certain conditions very hard to treat, it is worth noting that not all biofilms are bad. Many of the good probiotic species we need for optimal health also live in biofilms. For this reason, we must be discerning when choosing to treat biofilms.
Why Gut Biofilms Matter for Digestion, Immunity, and Chronic Symptoms
So, why do biofilms matter? We have many antibiotics, antifungals, and antiparasitics that can kill dangerous microbial infections in our intestines, right?
The truth is that these drugs are not foolproof. These drugs tend to work amazingly when microbes are free-floating but do not work nearly as well when the pathogenic microbes are in a biofilm. In fact, biofilms can make bacteria 1000 times more resistant to antibiotics!
The goo that surrounds the microbes literally prevents the antibiotic from being able to touch the bacteria at all. If antibiotics do penetrate the goo, many of the microbes in biofilms have developed specialized efflux pumps that spit the antibiotics back into the intestine.
Within biofilms, bacteria are also able to communicate with one another through various mechanisms. Gene transferring allows bacteria to share antibiotic resistance genes which can make the entire biofilm community antibiotic resistant.
Another form of communication, known as quorum sensing, allows the microbes to communicate with each other and coordinate biofilm formation. Essentially this allows for the microbes to build a strong biofilm and communicate when resources are needed in a specific area.
For all of these reasons, biofilms can significantly complicate the treatment of ailments within the digestive tract. They make it difficult to treat infections and control diseases like IBD, IBS, SIBO, and even other diseases like rheumatoid arthritis.
How Biofilms Contribute to Gut Dysbiosis and Chronic Health Issues
As previously discussed, biofilms are highly complex and can make treatment of various diseases incredibly difficult. In this section, I will take a deep dive into the science of exactly how this works. If you are a science nerd, pay attention!
Biofilms and Bacterial Resistance: Why Gut Microbes Become Harder to Remove
Let’s first discuss the exact architecture of a biofilm. That is, how they are created and what do they look like?
Step 1: Adhesion
Biofilms first start with free-floating (planktonic) bacteria. A bacteria will attach to the mucus layer of the intestine. This attachment is weak and can easily be broken.
Step 2: Microcolony
A few attached bacteria begin to produce extrapolymeric substances (EPS) that are a combination of complex carbohydrates, proteins, and extracellular DNA. This envelops the microcolony in the EPS goo that allows for initial communication between bacteria.
Quorum sensing is the first form of communication that starts in the microcolony. Quorum sensing allows for bacteria and other microbes within the microcolony to estimate population density and act accordingly.
Step 3: Maturation
The microcolony begins to mature into a full-sized colony of microbes. A mature biofilm can engage in many complex processes like horizontal gene transfer (sharing genes between microbes) which allows for biofilms to become antibiotic-resistant.
Mature colonies can also house dormant, spore-like pathogens, known as persister cells. Persister cells are incredibly resistant to pharmaceutical treatment and can wake back up once treatment is over. This allows for infections, like E. coli, to evade treatment and persist.
In this way, mature biofilms can cause antibiotic resistance and create a safe space for pathogens to become dormant and wait out antibiotic treatments.
Step 4: Dispersal
The last stage of biofilm formation is dispersal. In this stage, a chunk of the biofilm, or an individual bacteria, can break off and form another biofilm elsewhere in the digestive tract.
Biofilms Trap Bile Acids and Disrupt Gut Motility
Bile acids are digestive fluids made by the liver and stored in the gallbladder. Their main job is to break down fats and help absorb fat-soluble vitamins like A, D, E, and K. But that’s not all they do. Bile acids also keep gut bacteria in check, stimulate motility, and prevent toxins from building up.
When bile acids are flowing properly, they help clear out waste, prevent bacterial overgrowth, and support a healthy gut lining. But when something interferes with their function, digestion slows down, bacteria start to take over, and inflammation rises.
How biofilms alter bile acid metabolism
Pathogenic biofilms trap and modify bile acids, throwing off their balance. This happens in a few ways:
- They physically bind bile acids, keeping them stuck in the gut instead of circulating properly. This means less bile is available to digest fats and regulate motility.
- Bacteria inside biofilms alter bile acids, turning them into forms that are irritating to the gut lining and promote inflammation. Some of these modified bile acids can trigger diarrhea (IBS-D), while others contribute to constipation (IBS-C).
- When bile acids get trapped, they lose their natural antimicrobial properties. This gives harmful bacteria a chance to grow, making conditions like SIBO and gut infections harder to treat.
The Link Between Biofilms and Chronic Infections
Biofilms make infections harder to treat by shielding bacteria, fungi (like Candida), and even viruses from antibiotics and the immune system. This protection allows pathogens to persist, multiply, and flare up even after treatment appears to work.
- C. difficile reinfections – Research shows that C. difficile spores get trapped inside biofilms, allowing them to survive antibiotics and reactivate later. This explains why C. diff relapses are so common, even after treatment.
- H. pylori infections – H. pylori, the bacteria behind stomach ulcers, form biofilms in the stomach lining, making antibiotics far less effective. This allows the infection to linger and cause ulcers to return.
- Chronic UTIs – E. coli and other UTI-causing bacteria use biofilms to stick to the bladder lining and resist antibiotics. Even after symptoms clear, dormant bacteria can reactivate, leading to recurring infections.
- If you have ever heard that cranberry juice is good for UTIs, it is because special molecules in cranberries can help prevent biofilms from forming in the bladder!
How Biofilms Contribute to Inflammation and Autoimmune Triggers
Biofilms don’t just protect bacteria—they also fuel chronic inflammation and disrupt immune balance. When biofilms persist in the gut, they can trigger immune system overreactions, increase gut permeability (leaky gut), and contribute to autoimmune diseases like Crohn’s, ulcerative colitis, and rheumatoid arthritis.
The Link Between Biofilms and Chronic Inflammatory Conditions
- Crohn’s Disease & Ulcerative Colitis (IBD) – Research has found that biofilms are more common in people with inflammatory bowel disease and may be a major driver of symptoms. They trap harmful bacteria, trigger immune responses, and increase gut inflammation, making flares worse.
- Rheumatoid Arthritis (RA) – Gut biofilms can contribute to immune system dysregulation, which may lead to systemic inflammation and autoimmunity. Some studies suggest that bacterial biofilms in the gut can influence the development of RA by driving chronic immune activation.
How Biofilms Influence Immune Dysfunction & Leaky Gut
- Biofilms Disrupt Gut Barrier Function – Biofilms can thin the protective mucus layer in the gut, making it easier for bacteria and toxins to pass through the intestinal wall (leaky gut). This triggers chronic inflammation and an overactive immune response.
- Persistent Immune Activation – The immune system recognizes biofilms as a threat but struggles to eliminate them. This constant low-grade immune activation can contribute to autoimmune flare-ups and systemic inflammation.
The Functional Medicine Approach to Gut Biofilm Balance: A Smarter Strategy
With everything said so far, it should be clear that acknowledging biofilms is incredibly important to the treatment of many digestive system issues. However, it is not as simple as taking a handful of “biofilm busters” and calling it a day.
Why “Biofilm Busting” Alone Isn’t the Answer
As I alluded to at the beginning of this article, not all biofilms are bad. Many of the beneficial bacteria we need for vitamin synthesis, immune system regulation, metabolism, and digestion require biofilms for their own survival.
If we indiscriminately dissolve and remove all biofilms, then we may end up doing more harm than good. For this reason, biofilm treatment must be about removing “bad” biofilms and preserving the “good” biofilms.
A Step-by-Step Approach to Restoring Healthy Gut Biofilms
Balancing biofilms effectively is difficult and can be the reason why many treatment plans fail. As such, I have created a 4 step process for removing “bad” biofilms while promoting the growth of “good” biofilms.
Step 1: Prevent Pathogenic Biofilms from Forming
The first step is to optimize the terrain. It is difficult for pathogenic biofilms to take over in a healthy intestinal environment. As such, it is incredibly important to optimize intestinal health as the first step.
In some cases, this step is enough to remove biofilms. Regardless, this step is important for preventing problematic biofilms from reforming after treatment.
The two areas to focus on here are bile flow and gut motility:
Bile flow:
Bile is a natural antimicrobial and biofilm disruptor that helps flush out pathogens and toxins from the gut. Supporting bile production ensures a steady flow that prevents biofilms from sticking.
- Amino acids (Taurine & Glycine) – These amino acids help thin bile, making it more effective at breaking down fats and biofilm structures.
- Taurine: Found in seafood (scallops, shrimp, tuna), dark meat poultry, eggs, and dairy.
- Glycine: Found in bone broth, collagen, gelatin, soy, poultry skin, and organ meats.
- Bitters – Herbal extracts and bitter foods help stimulate bile production, promoting digestion and optimal gut health
- Take a dropper of digestive bitters 10–15 minutes before meals.
- Eat bitter greens (arugula, dandelion, endive, radicchio, kale) with meals to stimulate bile flow.
Gut Motility:
Keeping things moving is just as important as breaking things down. A sluggish gut allows biofilms to build up, while steady motility helps sweep them out.
- Mindfulness – The gut and brain are directly connected, and stress slows digestion. Taking time to relax before meals, eating without distractions, and engaging in deep breathing can support vagus nerve activation and natural motility.
- Prokinetics – These compounds help trigger peristalsis, the wave-like contractions that move food and waste through the digestive tract. They’re especially useful for people prone to sluggish digestion or constipation.
- Ginger – Can be taken as tea, fresh slices, or a supplement before meals.
- Motility-supporting herbs – Iberogast, artichoke extract, and triphala can gently encourage movement without being too harsh.
- Magnesium citrate – Helps relax the muscles of the gut, supporting motility.
Step 2: Gently Weaken Harmful Biofilms Without Disrupting the Gut Lining
After the stage has been set with step one, it is time to start physically breaking down biofilms. I typically address this process in three distinct domains:
Quorum sensing inhibition:
Bacteria communicate with each other to coordinate biofilm formation. By interfering with these signals, we can prevent biofilms from reinforcing themselves and make them more vulnerable to removal.
- Garlic – Contains allicin and other beneficial compounds, which block bacterial signaling and help disrupt biofilm structure. Read this article on allicin for more information.
- Green Tea – Rich in EGCG, a natural quorum sensing inhibitor that helps weaken biofilms and prevent new ones from forming.
- Cranberry – Prevents bacteria from sticking to surfaces, making it harder for biofilms to attach to the gut lining.
- Plantain Leaf – A mucilage-rich herb that protects the gut lining while interfering with biofilm formation.
- Turmeric – Contains curcumin, which disrupts bacterial communication and reduces inflammation that can worsen biofilm overgrowth.
Extracellular matrix degradation:
Biofilms are held together by a sticky matrix of proteins, polysaccharides, and extracellular DNA (eDNA). Breaking down this matrix makes biofilms more permeable and easier to remove.
- N-acetyl cysteine (NAC) – A precursor to glutathione that breaks down biofilm sulfide bonds and makes them more fragile.
- Serratiopeptidase – A proteolytic enzyme that digests biofilm proteins, helping to dissolve their protective layers.
- Ethylenediaminetetraacetic acid (EDTA) – A chelating agent that binds calcium and magnesium in biofilms, making them structurally weaker.
- EDTA is a strong chelator that can also bind essential minerals, so it should be used cautiously and under professional guidance to avoid depleting important nutrients.
Efflux pump inhibition:
Efflux pumps are like toxic waste disposal systems for bacteria—they pump out antimicrobials and keep biofilms resistant to treatment. Blocking these pumps makes bacteria more susceptible to removal.
- Berberine – A powerful efflux pump inhibitor that also has antimicrobial and anti-inflammatory properties.
- Japanese Knotweed – Rich in resveratrol, which inhibits bacterial resistance mechanisms and weakens biofilm defenses.
- Thyme – Contains thymol, a natural efflux pump inhibitor that makes bacteria more vulnerable to biofilm disruptors.
Step 3: Safely Disperse and Remove Biofilms from the Gut
Once the biofilms are broken down, it is important to get them out of the intestines as soon as possible. This typically requires some sort of binder combined with good hydration, optimal fiber intake, and a daily bowel movement.
Daily bowel movement
- Fiber – Consuming around 30 grams of fiber per day is typically recommended for optimal health and bowel regularity. However, it may be difficult to consume high-fiber foods in the case of SIBO.
- Water – We should all be aiming for about 2.5-4 liters of water per day (depends on age and sex). Water lubricates the bowels and provides adequate blood flow for proper digestion.
- Movement – A sedentary lifestyle can cause constipation in and of itself. 150 minutes of cumulative exercise per week along with regular movement (walking, going to the bathroom, etc.) every hour or so is adequate.
Binders
Once biofilms start breaking down, they release toxins, bacteria, and heavy metals into the gut. Binders help trap and remove these waste products so they don’t get reabsorbed and cause symptoms.
- Activated charcoal – Best for gas and toxin absorption; ideal for quick relief from bloating and digestive discomfort but can be constipating if overused.
- Zeolite – Strongest for heavy metal detox; binds ammonia and environmental toxins, making it a good choice for those with toxin overload or mold exposure.
- Psyllium fiber – Best for gentle bulk cleansing; helps physically remove biofilm debris while supporting regularity and microbiome balance.
- Citrus pectin – Ideal for sensitive individuals; binds toxins without disrupting minerals or gut bacteria, making it a gentle option for daily use.
Step 4: Strengthen Beneficial Biofilms to Restore Gut Homeostasis
The last step for addressing the gut is to support beneficial biofilms. Beneficial bacteria and yeast can prevent the recurrence of pathogenic biofilms and ensure lasting benefits from biofilm treatment. I address this step in three major ways.
Probiotics
- Competition – A good probiotic blend should contain beneficial bacteria that can take up space and make it difficult for negative bacteria to find a place to grow. The major species are as follows:
- Bifidobacterium bifidum
- Bifidobacterium longum
- Lactobacillus reuteri
- Disruption – Many probiotic species will also break down other biofilms to ensure their own survival. A handful of these species are also beneficial for our health. As such, we can leverage them to break down biofilms on our behalf:
- Bacillus subtilis
- Saccharomyces boulardii
- Lactobaacilus rhamnosus GG
- Renewal – We also want to work with probiotics that restore the gut lining and promote beneficial biofilms to support our health. Below are some of the best strains for this work:
- Bifidobacterium breve
- Akkermansia muciniphila
- Faecalibacterium prausnitizii
Prebiotic fibers
Prebiotics act as fuel for beneficial biofilms, helping good bacteria thrive while making it harder for pathogenic ones to return. Without prebiotic support, even the best probiotic strains may struggle to establish a lasting presence in the gut.
- Inulin – A fermentable fiber found in onions, garlic, and chicory root that selectively feeds Bifidobacteria, helping to crowd out unwanted microbes.
- Acacia fiber – A gentle, soluble fiber that nourishes gut-protective bacteria without causing bloating, making it ideal for sensitive individuals.
- Root decoctions – There are many recipes for delicious root decoctions containing herbs like chicory, dandelion, burdock, elecampane, and ashwagandha, amongst others. Here is my favorite root decoction recipe.
Polyphenols
Polyphenols aren’t just antioxidants—they actively shape the gut microbiome by encouraging beneficial biofilms and inhibiting harmful bacterial growth.
- Berries – Rich in flavonoids that promote beneficial gut bacteria while preventing pathogenic adhesion. Blueberries, raspberries, and pomegranates are among the best options.
- Hibiscus tea – A natural source of anthocyanins and tannins, which help modulate gut bacteria and reduce inflammation.
- Green tea – Contains EGCG, a compound that supports beneficial bacteria while disrupting quorum sensing in harmful bacteria.
What About Antibiotics, Antimicrobials, and Probiotics?
I know what you’re thinking… What about antibiotics and antimicrobials? Why did I not talk about oregano oil and Rifaximin? Don’t we need to kill all of those biofilm-forming pathogens to fix gut dysbiosis?
Well, kinda sorta…
When to Use Antibiotics or Herbal Antimicrobials
For some infections, antibiotics are non-negotiable. If you have a confirmed bacterial infection—like C. difficile, H. pylori, or a UTI—your provider may prescribe specific antibiotic protocols to properly clear the infection. In these cases, biofilm removal can support treatment, but antibiotics remain the primary tool for eliminating the infection safely.
Then there’s the gray area—conditions like SIBO, gut dysbiosis, and overgrowth of pathogenic bacteria where people often reach for herbal antimicrobials like oregano oil, berberine, or allicin. While these can be effective, the problem is that antibiotics and antimicrobials don’t work well against bacteria hiding in biofilms.
How biofilms make antibiotics less effective
Biofilms act like armor that shields bacteria from treatment. Even if an antibiotic or antimicrobial reaches the infection site, biofilms can:
- Block the drug from penetrating the biofilm layer, meaning only surface bacteria get exposed.
- Activate efflux pumps, which bacteria use to push antibiotics and antimicrobials back out before they take effect.
- House dormant bacteria (persister cells) that survive treatment and reactivate later, leading to reinfection and relapse.
This is why antibiotics alone often fail and why so many people experience recurring gut infections, SIBO relapses, or antibiotic-resistant bacteria.
Conclusion: The New Functional Medicine Paradigm for Gut Biofilm Balance
Biofilms are the missing piece in understanding chronic gut issues like IBS, IBD, SIBO, and dysbiosis. They protect harmful bacteria, disrupt digestion, fuel inflammation, and make infections harder to treat. But the solution isn’t just about “busting” biofilms—it’s about balancing them, removing the harmful ones while supporting the beneficial ones that help maintain gut health.
By following a targeted, step-by-step approach, we can:
- Break down harmful biofilms without damaging the gut lining.
- Support digestion and bile flow to prevent biofilm buildup.
- Use biofilm disruptors alongside antimicrobials for better treatment success.
- Restore beneficial biofilms to promote long-term gut balance.
If you’ve been struggling with gut issues that won’t resolve, it might be time to look deeper. Let’s figure out what’s really going on with your gut health.
Book a free 15-minute discovery call today, and let’s talk about how we can create a plan that actually works.
References
- Active Thrombin Produced by the Intestinal Epithelium Controls Mucosal Biofilms
- Archaea Influence Composition of Endoscopically Visible Ileocolonic Biofilms
- Biofilms and Benign Colonic Diseases
- Campylobacter Biofilm Formation
- Digestive Exophagy of Biofilms by Intestinal Amoeba and Its Impact on Stress Tolerance and Cytotoxicity
- Gastrointestinal Biofilms: Endoscopic Detection, Disease Relevance, and Therapeutic Strategies
- Gut Biofilms: Bacteroides as Model Symbionts to Study Biofilm Formation by Intestinal Anaerobes
- Gut Goo: Physiology, Diet, and Therapy of Intestinal Mucus and Biofilms in Gastrointestinal Health and Disease
- Intestinal Biofilms: Pathophysiological Relevance, Host Defense, and Therapeutic Opportunities
- Interactions Between Host and Intestinal Crypt-Resided Biofilms Are Controlled by Epithelial Fucosylation
- Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis
- Bacterial Biofilms: Novel Strategies for Intestinal Colonization by Probiotics
- Probiotic Profiling of Bifidobacteria Indigenous to the Human Intestinal Mucosa Shows Alleviation of Dysbiosis-Associated Pathogen Biofilms
- Salmonella Biofilm Formation, Chronic Infection, and Immunity Within the Intestine and Hepatobiliary Tract
- Gut Microbiota Biofilms: From Regulatory Mechanisms to Therapeutic Targets
Justin Perr is a Registered Dietitian and Certified Functional Medicine Practitioner specializing in weight loss and gut health. He helps patients uncover root causes and achieve lasting results with science-backed nutrition.
