Biofilm in the Gut: Understanding and Treating This Common Issue

What Is Biofilm in the Gut?

Gut biofilm is a community of microorganisms which stick to each other and also to the mucus lining of your gut. They naturally grow throughout your gastrointestinal tract.

These microbial communities are encased in extracellular polymeric substances (EPS, which contains polysaccharides, proteins, and lipids), secreted by these microbes into their surrounding environment, forming a slimy matrix.

In the gut, biofilms help protect beneficial bacteria and maintain microbial balance. However, when pathogenic bacteria dominate and form a biofilm, it becomes harmful, as it provides a barrier that shields these bad bacteria against your immune system and antibiotics, making them hard to treat.

Functions of Biofilm

Gut biofilms have many functions, including:

• Protection against pathogens.
• Maintenance of gut microbial balance.
• Exchange of nutrients between your body and gut microbiome.
• Regulation of immune responses.
• Facilitation of microbial communication.

When Does Biofilm Become Problematic?

Gut biofilm can cause problems when these protective barriers are built by harmful microbes, making infections harder to treat.

• Biofilms act as a shield, preventing your immune system or antibiotics from destroying pathogenic microbes, making the infections chronic and also causing antibiotic resistance.
• A strong pathogenic biofilm can lead to harmful gut bacteria outnumbering the beneficial ones, causing an imbalance in the gut microbiome diversity called dysbiosis.
• Some harmful microbes that form biofilms may release toxic substances into their surroundings, causing food poisoning, inflammation, or infections.

Causes of Biofilm Overgrowth in the Gut

While biofilm is generally beneficial, it can become problematic in certain situations, such as when it is formed by harmful bacteria. Here’s what causes it:

Poor Diet:

• A diet consisting of more processed, fatty and high-sugar foods can cause harmful gut bacteria to overgrow.

Antibiotic Overuse:

• Excessive use of antibiotics without a doctor’s prescription can cause imbalances in your gut microbiome, causing the number of beneficial bacteria to fall and harmful microbes to dominate.

Chronic Stress:

• Stress can affect your gut through the gut-brain axis, disrupting the gut microbiome balance and weakening the immune system, promoting biofilm overgrowth.

Impaired Gut Motility:

• When food and waste remain in the digestive tract due to impaired gut motility, the biofilm can build and collect.

Underlying Conditions:

• Conditions include SIBO, candida overgrowth, or leaky gut syndrome, which can cause gut biofilm overgrowth by providing an environment fit for the spread of dangerous bacteria.

Symptoms of Gut Biofilm Imbalance

When dangerous gut biofilms form, they can impact your immunity, digestion, and overall health, resulting in symptoms such as: 

• Abdominal bloating and gas. 
• Indigestion and nausea. 
• Chronic diarrhoea or constipation. 
• Acid reflux, sour belching, and heartburn. 
• Food intolerances and sensitivities. 
• Infections occur frequently and are difficult to heal from. 
• Fatigue, mental fog, and difficulties concentrating. 
• Joint pain as a result of inflammation. 
• Skin disorders like eczema, acne, and psoriasis. 
• Unintentional weight loss due to nutritional inadequacies. 
• Symptoms that remain despite treatment.

Diagnosing Gut Biofilm Impairment

Getting the right diagnosis is a key aspect of healthcare. The methods and new technologies involved in the diagnosis of gut biofilm overgrowth are:

Medical History and Symptoms:

• To understand your health status, your doctor takes a detailed medical history and asks about your symptoms and other details like the history of infections or antibiotic use.

Stool Tests:

• Stool samples may be analysed in a lab to look for the presence of pathogenic microbes, providing insight into their overgrowth. Microscopic studies of stool samples can help visualise the biofilm structures directly.

SIBO Breath Test:

• This non-invasive test measures the quantity of hydrogen and methane you breathe out after you drink a mixture of water and non-digestible sugars like lactulose. This is used to diagnose bacterial overgrowth in the small intestine.

Advanced Tests:

• The Tube Biofilm Formation (TBF) test is done to identify specific strains of harmful microbes that cause the overgrowth of gut biofilm.
• Polymerase Chain Reactions (PCRs) are used to identify certain infections and find genes linked to biofilms.
• A Comprehensive Digestive Stool Analysis (CDSA) is performed to analyse your stool sample for bacteria, parasites, yeast, lipids, and digestive enzymes.

Treatments for Biofilm in the Gut

Why is the treatment for gut biofilm so important? Approximately 80% of chronic and recurrent microbial infections in the human body are due to bacterial biofilm. Proper diagnosis and treatment can help disrupt these biofilms, maintain gut microbial balance and improve your overall gut health.

1. Disrupting the Biofilm

Imagine trying to peel a stubborn sticker that has been stuck for years. It doesn’t come off in one pull, right? Even if you manage to do so, the adhesive stays firmly attached. 

Just like the sticker, the gut biofilm is not easy to remove either. The harmful bacteria that form this layer are protected by a slimy matrix, making them harder to remove, even with the use of antibiotics. 

Biofilm disruptors are specific enzymes that break down the protective matrix surrounding the harmful microbes, thereby exposing them and making them easier to eliminate. Examples of biofilm disruptors are N-acetylcysteine (NAC), serrapeptase, and lumbrokinase.

Another group of medications called chelating agents (like EDTA) bind to and remove minerals like iron, calcium, and magnesium, which microbes use to strengthen their biofilm matrix.

2. Eradicating Harmful Microbes

These methods help kill the harmful microbes that form gut biofilm:

Antimicrobials:

• Antimicrobials are used to kill the harmful microbes hiding within the gut biofilm. You may choose natural antimicrobial options like berberine, neem, oregano oil, or garlic extract. In severe cases, you’ll need prescription antibiotics or antifungals, but they must be paired with biofilm disruptors to give the desired results.

Probiotics:

• Probiotics are live microorganisms that have health benefits when consumed. Taking probiotics as food (fermented foods like yoghurt, kefir, sauerkraut, kimchi or tempeh) or as supplements introduce beneficial bacteria into your gut, preventing the overgrowth of harmful microbes. Choose probiotic supplements that contain good bacteria, like lactobacillus and bifidobacterium.

3. Supporting Gut Health

Improving gut health helps to dislodge biofilm in the gut, thus restoring a balance of gut microbes.

Prebiotics:

• These are special fibres found in foods like onions, garlic, leeks, asparagus, and whole grains, which act as a food source for beneficial gut bacteria. Consuming prebiotics supports the growth of good bacteria in your gut.

Dietary Changes:

• Avoid foods that may cause irritation of the gut lining, such as processed, oily, and sugary foods. This will effectively starve some bad gut microbes, thus cutting down on their growth rate. You will further improve overall gut health if your diet and way of eating focus more on anti-inflammatory foods, such as whole grains, fresh fruits and vegetables, and other healthy options.

Hydration:

• Drink enough water to help get proper gut motility and flush out toxins released from the disrupted biofilm in the gut.

4. Strengthening the Immune System

The strong biofilm matrix forms a shield between your immune system and harmful gut microbes. By strengthening your immunity, your body can recognise and eliminate harmful microbes hidden within the biofilm and also prevent reinfection.

Stress Management:

• Even though stress primarily affects your mind, relieving it through techniques like yoga, meditation, and breathing exercises can improve gut health and reduce gut inflammation through the communication between your brain and gut, called the gut-brain axis.

Nutritional Support:

• Identify and correct nutritional deficiencies by including necessary vitamins and minerals, especially vitamin D, zinc, and magnesium, to boost your immunity.

But before anything, it's important to know what your gut type it, so that your remedies and treatments can be personalised.

What Type of Gut Do You Have?
Take Quiz

Natural Remedies for Biofilm Management

Natural remedies for managing and preventing biofilm overgrowth include the use of plant extracts and herbs that have antimicrobial and anti-inflammatory properties. Here are some easy remedies you can try out at home:

Apple Cider Vinegar:

• Studies have shown that apple cider vinegar inhibits the growth of certain harmful microbes in the gut and has an antibiofilm activity (the ability to stop the formation and growth of biofilms).
• How do you use it? Dilute 1 to 2 tablespoons of apple cider vinegar in 250 ml of water and consume it orally before meals.

Garlic:

• The organosulfur compounds of garlic, like allicin, have antibacterial properties and penetrate the biofilm layer, eliminating a wide range of bacteria, including multi-drug resistant strains.

Turmeric:

• Curcumin, a phytochemical derived from turmeric, has antibacterial and antibiofilm activity. Curcumin makes bacteria sensitive to antibiotics, making it easier to treat them.

Ginger:

• Ginger extract effectively inhibits biofilm formation. Studies also showed that biofilm disruptors work better in detaching biofilms when ginger extract is administered alongside them.

Long-Term Strategies for Preventing Biofilm Overgrowth

Biofilms formed by good gut bacteria are beneficial, while a harmful gut biofilm formed by pathogenic bacteria can lead to inflammation, infection, and digestive issues. How can you prevent harmful gut biofilm overgrowth? Here are some useful tips for you:

Maintain a Balanced Diet:

• Include foods that are good for gut health, like fibre-rich whole grains, fruits, and vegetables, and prebiotic-rich foods like garlic, onions, bananas, and leafy greens, and limit the intake of processed, sugary, and oily foods.

Regular Probiotic Use:

• Including fermented foods in your diet, like yoghurt and kefir, can improve the diversity of beneficial bacteria in your gut. Choose fermented foods which are labelled “live and active cultures” to ensure they contain live beneficial microbes.

Limit Antibiotics:

• Limit antibiotic use and avoid self-medication. To avoid gut microbiota abnormalities, always take probiotics after taking antibiotics.

Stay Active:

• Exercise regularly to support gut motility, prevent constipation, and improve gut microbial diversity.

Hydration and Detoxification:

• Drink plenty of water to support the digestive process and to flush out toxins and wastes from your gut.

The Bottom Line

Gut biofilms are a natural occurrence that protects gut microbes from chemicals and other environmental causes that may disrupt their balance. However, it may become problematic when harmful gut bacteria form biofilms, making it hard for your immune system and medications to eradicate them. 

Medications like biofilm disruptors and antimicrobial agents can be used to kill pathogens while you restore gut microbial diversity through a healthy diet rich in probiotics and prebiotics, as well as lifestyle adjustments.