Fungi in the gut: what is true about Candida

Healthy state

Besides bacteria, the gut is home to fungi, mainly yeasts. They are only a small part of the 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” by number, but almost everyone carries them. In a large analysis of 317 stool samples from healthy adults, baker’s yeast (Saccharomyces cerevisiae) turned up in about 97 percent of samples, Malassezia (otherwise more of a skin fungus) in 88 percent and Candida albicans in 81 percent. Candida in the stool is therefore the normal case, not a warning sign. Some of the yeasts come from bread, beer or yogurt and simply pass through.

Unlike the bacterial microbiome, the fungal microbiome is not very diverse and is very unstable. In the same person, samples taken over a year often differ as much as samples from different people. That is also why it has not been defined what a “healthy” fungal microbiome looks like. A single stool test is a snapshot and says very little about health.

Fungi are kept small from two sides. First by bacteria, above all the oxygen-avoiding kinds such as clostridia and Bacteroides: in mice, they prompt gut cells to make a defence peptide of their own (LL-37, called CRAMP in mice) that stops Candida from settling. Adult mice with an intact gut flora therefore carry hardly any Candida, but do after antibiotics. Second by the immune system of the gut lining, which has to tell whether a yeast is just living alongside us or invading tissue. Candida can take two forms. The round yeast form is harmless. The thread form (hyphae) invades tissue and makes a toxin peptide, candidalysin, that damages cells. In healthy people it almost always stays in the yeast form.

Food plays a part too. In a study of 98 people, a lot of Candida in the stool went with a high-carbohydrate diet in the preceding days, and little Candida with more protein and fat. That is an observation, not proof that sugar “feeds” Candida and a diet drives it out. It rather shows how quickly the fungal microbiome shifts with food. The same study found the methane producer Methanobrevibacter, an archaeon rather than a fungus, in about 30 percent of people, also more often on a high-carbohydrate diet.

Disrupted state: causes and effects

Candida becomes a problem when the balance tips. The most common triggers are antibiotics (the bacteria that act as opponents are missing), corticosteroids and other drugs that dampen the immune system (the gut lining’s defence is weakened), diabetes with high blood sugar, chemotherapy, and severe illness with catheters or ventilation. In intensive care patients, Candida can pass from the gut into the bloodstream and become life-threatening. That the gut can be the entry point is why research takes an interest in gut colonisation.

The typical infections are visible elsewhere, though: oral thrush with a white coating that can be wiped off (especially in babies, older people, denture wearers and after inhaled corticosteroids), thrush in the oesophagus with pain on swallowing, vaginal yeast infection with itching and discharge (more common in pregnancy, after antibiotics and with diabetes), and fungal infection in moist skin folds. Anyone with repeated vaginal yeast infections needs their own work-up; whether the gut plays a role is being researched and is open.

The popular “Candida syndrome” is not among them. Long symptom lists circulate online, from tiredness through bloating and skin problems to sugar cravings. There is no evidence for this, and the leap from a stool result is wrong anyway: if four out of five healthy people have Candida albicans in the stool, a “positive” result cannot indicate disease. Anyone who gets bloated after sweet foods or bread far more often has a sugar intolerance (fructose, lactose, hard-to-digest sugars) or irritable bowel than a fungus. Sugar cravings, too, have many other causes.

There is one serious but disputed exception: fungal overgrowth in the small intestine (SIFO). In two studies, researchers found fungi in a small-intestine sample in about a quarter of people with unexplained digestive symptoms (belching, bloating, fullness, nausea, diarrhoea). A sluggish small-bowel movement and acid blockers count as risks. Whether the fungi really cause the symptoms and whether antifungal treatment helps is open. It cannot be shown in stool, only in a small-intestine sample taken during an endoscopy.

In inflammatory bowel disease Inflammatory bowel disease Umbrella term for Crohn’s disease and ulcerative colitis: long-term, relapsing inflammation of the gut that needs medical treatment. More in the chapter “Immune system and inflammation”, the fungal microbiome is seen to be shifted. In a study of 235 patients and 38 healthy people, the share of Candida albicans was higher and that of baker’s yeast lower, and the interplay between bacteria and fungi was disturbed. In Crohn’s disease, antibodies against yeast are also known and serve as a lab marker. Whether the fungi help drive the inflammation or simply benefit from the inflamed lining is not settled. An anti-fungal diet or fungal treatment is therefore not supported for these diseases.