WE ARE all a bit mouldy – literally. Our bodies are home to a great many fungi. They are scattered on our skin, inside our mouths and in our guts. Some of them have adapted so well to life in the human body that they can’t survive anywhere else. But we know very little about this “mycobiome” and what it is doing.
We know the fungi are there and we have read their DNA, but in the past it hasn’t been clear if they offer us any benefits or are mainly passive hitchhikers, with the odd infection-causing interloper. Now, though, a boom in interest in the bacteria that reside in our guts has spurred researchers to take a new look at fungi too, with an eye to unravelling the secrets they hold.
What they are finding is that our fungal residents can have a significant influence on our health, raising the prospect that we could manipulate them to boost our resilience against disease.
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The good news is that we aren’t starting from scratch. For a start, we know that the fungi in our bodies are less diverse than the bacteria within us, probably by around a factor of 10, says at McMaster University in Ontario, Canada. We also know that certain fungi crop up consistently. For instance, a genus of yeast called Malassezia makes up the majority of the species on our skin, says Kalan.
What does the mycobiome do?
Until recently, the extent to which our mycobiomes differed was largely unknown. But new evidence suggests they can vary to a significant extent, particularly as we age, with implications for our risk of certain diseases. A 2023 study . Certain groups of fungi had a strong age preference – for instance, one group dominated by Candida was more likely to be found in older people, where it was linked with an increased risk of multiple diseases associated with a compromised intestinal barrier, such as some cancers, bowel disease and diabetes. Similarly, in work described in his book Total Gut Balance, at Case Western Reserve University in Cleveland, Ohio, identified six such groups of gut mycobiome.
Every fungal species in our bodies is arguably a “pathobiont”, meaning they all have the potential to cause infection, says Kalan. However, the risks they pose depend both on the species and on our own level of vulnerability: a fungus that is a minor inconvenience for one person can be lethal for someone else.
One of the most dramatic examples is a yeast called Candida auris, which was . Since then, it has spread at an alarming rate, primarily in healthcare facilities, where it has found many hosts with weakened immune systems. It is resistant to an increasing number of treatments, which helps explain why mortality rates are estimated at 30 to 60 per cent. “The prevalence of infection is very low,” says Kalan, “but it’s still a very high risk if you do end up with one of these infections.”
There is also evidence that gut fungi can exacerbate and prolong viral infections, such as covid-19. Recently, a team led by at Cornell University in New York found that people with severe covid-19 also . This triggered an explosion of white blood cells called neutrophils, which are a vital part of the immune response, but can make it harder to recover from illnesses when present in high numbers. This immune system signature could still be detected a year later. “There is a link with long covid, but it’s not like the fungus is causing the long covid,” stresses Iliev. Instead, the two are interacting in some way that we have yet to fathom.
Fungi and chronic diseases
We are, however, developing a better understanding of how changes to gut fungi can affect other conditions. For instance, Ghannoum and his colleagues have found that interactions between gut bacteria and fungi can play a role in Crohn’s disease. When living alongside certain bacteria, a normally benign fungus called Candida tropicalis starts to form tiny thread-like structures called hyphae that release enzymes and absorb nutrients. “We found it starts to poke holes in the gut lining,” says Ghannoum. Similarly, in 2022, Iliev’s team showed that some strains of C. albicans in the gut are involved in inflammatory bowel disease.
Kalan is also investigating how fungi and other microbes interact on our skin. Her group studies chronic wounds like diabetic foot ulcers, which heal very slowly. The team found that C. albicans in such wounds can be triggered to form hyphae by bacteria called Citrobacter freundii. This leads to more severe infections and inflammatory responses.
There are even tentative links between our mycobiome and cancer. In 2017, Ghannoum’s team found that people with a particular kind of tongue cancer had an unusual mix of microbes in their mouths: the bacterial and fungal communities were both altered compared with those in people without this cancer. But the researchers don’t know what the causal mechanisms are, which Ghannoum says is typical of fungus-cancer studies. “A lot of it is still correlation.”
At this point, it may seem like our mycobiome is nothing but a source of problems. However, fungi can be beneficial, at least some of the time. The yeast Saccharomyces boulardii helps prevent antibiotic-associated diarrhoea, for instance, and the related baker’s yeast S. cerevisiae can control vaginal thrush by suppressing C. albicans.
How do you keep your mycobiome healthy?
There are sure to be more benefits, but we haven’t paid much attention to the upsides of bodily fungi. “A lot of focus has been on how are they making us sick and how is it contributing to other diseases,” says Kalan.
But we may yet conclude that we can manipulate the mycobiome for the benefit of our health. Like the bacterial arm of our microbiome, the make-up and diversity of fungi in our gut . Carbohydrate-rich food is correlated with an increase in Candida species, for example. We are far from being able to recommend a mycobiome-boosting diet, but given the impact our , it is likely that we will start seeing such research soon.
