Biofilms in the gut and “biofilm busters”

Healthy state

A biofilm Biofilm A community of microbes that sticks to a surface and embeds itself in a self-made protective coat, such as dental plaque. is a community of microbes that sticks to a surface and embeds itself in a self-made coat of sugars, proteins and DNA. This is how bacteria mostly live in nature, not as single free-floating cells. The coat protects them from drying out, immune cells and antibiotics.

The best-known example is dental plaque. It quickly forms again after brushing and is removed mainly mechanically, with a brush and floss. In medicine, biofilms on catheters, artificial joints and heart valves are feared: there, bacteria survive antibiotics, and the foreign material often has to come out.

In the healthy gut, too, some bacteria live in biofilm-like communities, for example on food particles and in the outer, loose mucus layer Mucus layer A gel layer of mucins on the gut wall that keeps bacteria at a distance. In the colon, the inner layer is almost free of microbes. More in the chapter “The mucus layer and additives” of the colon. The inner mucus layer stays largely free. This arrangement is normal and part of a healthy microbiome Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity”.

Disrupted state: causes and effects

In two European centres, doctors looked for yellow-green, firmly attached layers during 1426 colonoscopies. They found them in 57 percent of people with IBS Irritable bowel syndrome Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis” and 34 percent with ulcerative colitis, but in only 6 percent of controls, mainly at the end of the small intestine and in the right colon. Under the microscope these were dense bacterial films, often with many E. coli and Ruminococcus gnavus, and bile acids Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea” accumulated in them. That fits with bile acid diarrhoea.

This is an important but still young finding. Whether the layers are a cause or a consequence of symptoms is open, and other groups need to confirm it. The authors see it as support for the idea that bacteria in the small intestine help trigger IBS. The European and American neurogastroenterology societies, by contrast, consider this SIBO Small intestinal bacterial overgrowth (SIBO) Too many bacteria in the small intestine, where normally few live. Bloating and diarrhoea are typical; it is usually diagnosed with a breath test. More in the chapter “When the small intestine is too densely colonised”–IBS hypothesis unproven after 20 years.

In colorectal cancer, such biofilms were found in about half of patients and in around 13 percent of healthy people. In mice they triggered tumours. That is a reason to take bowel cancer screening seriously, not to fight biofilms on your own.

Online it is often said that stubborn SIBO, Candida or parasites hide in biofilms and therefore cannot be treated. “Biofilm busters” are recommended: N-acetylcysteine (NAC), enzymes such as serrapeptase or nattokinase, EDTA, bismuth and mixtures of these, usually before herbal protocols or antibiotics. In the lab, some of these substances break up biofilms. In the human gut this has not been shown, and a 2024 review considers effective treatments against gut biofilms not yet developed.

The most-cited analysis is a retrospective review of 13 medical records: with biofilm agents added to herbal antimicrobials, breath test Breath test After drinking a sugar solution, hydrogen and methane in the breath are measured several times. This can reveal sugar intolerances and signs of bacterial overgrowth. More in the chapter “Gut tests: what they show and what they do not” values fell more, but the share of people without a SIBO finding did not differ. For NAC, there are studies only as an add-on to Helicobacter treatment in the stomach; a Cochrane review could not say whether it helps.

The risks, on the other hand, are real. Serrapeptase and nattokinase dissolve fibrin, a component of blood clots. A person taking aspirin had a brain haemorrhage after a week of nattokinase. For serrapeptase, a systematic review found only methodologically weak studies and hardly any safety data. EDTA binds minerals such as calcium; deaths occurred with infusions. Bismuth is part of Helicobacter therapy; taken for a long time it can damage nerves and the brain.