Aspergillus, a fungus that lives on the healthy human body, but can also cause deadly infections. Wellcome Images
Aspergillus, a fungus that lives on the healthy human body, but can also cause deadly infections. Wellcome Images
ScienceThe Loom

Getting To Know Your Inner Mushroom

Leave a bagel on the counter for a few days, and you’ll probably notice purple splotches growing over it. At some point a mold spore wafted across the kitchen, landed on the bagel, and started to eat your food. Molds are a kind of fungus–just like toadstools, brewer’s yeast, and death cap mushrooms. They don’t just nosh on bagels. Fungi exist on all continents, and have been thriving for many hundreds of millions of years. Some break down the remains of animals and plants in the soil. Some provide nutrients to trees and crops through their roots, in exchange for a supply of carbon the plants make with sunlight. While fungi have evolved different shapes and sizes, they are all alike in some fundamental ways. When it comes to eating, for example, they are like inside-out animals. We animals swallow food and then break it down with enzymes. Fungi break their food down first by releasing enzymes, and then they absorb it.

In the abstract, fungi are impressive and fascinating. (Biggest organism on Earth? A fungus.) But as you get to know fungi in their full reality, there’s something disturbing about them that you have to learn to accept. You are loaded with them. Slathered. That bagel on the counter? That’s you.

So I understand if some readers at this point say, “You know what? I have some very important pots to scrub,” and switch off their iPhones. But for the rest of you–you hardy, curious few–let me give you a tour of your personal fungal garden.

This tour is based on decades of research carried out by many scientists. Originally, their research dealt almost exclusively in the fungi that make us sick. Fungal infections can range from bothersome to deadly. Athlete’s foot, caused by mold such as Trichophyton rubrum, typically does nothing more than makes the skin itch. But other fungi can explode in our bodies. In the 1980s, people whose immune systems had been decimated by HIV became overwhelmed with a fungus called Pneumocystis jiroveci. It took over their lungs and caused lethal pneumonia.

But we are hosts to fungi both in sickness and in health. Fungi are an important part of the microbiome, along with bacteria and viruses–the subject of my post on Monday. Like those other organisms, our fungi have made it tough to study them with their reluctance to grow in labs. So scientists are beginning to use a different strategy–dispensing with gardening fungi and just gathering fungal DNA from healthy people.

Today in Nature, Julie Segre of the National Human Genome Research Institute and her colleagues present the first comprehensive atlas of the fungi growing on our skin. They collected fungal DNA from 14 sites on the bodies of 10 healthy volunteers. They found fungi everywhere: not just on the soles of people’s feet, but on the palms of their hands, on their backs, and in their ear canals.

Most of the skin is dominated by a single genus of fungi, called Malassezia. Malassezia‘s closest relatives include corn smut, a fungus that brings misery to corn farmers. At some point in the past, however, the ancestors of Malassezia shifted from plants to humans, where they now feed on the fatty secretions released by our skin. Malassezia has evolved into at least 14 different species; Segre and her colleagues found 11 of them among the participants in their study.

In some places, like the nostrils or the back of the head, Malassezia rules supreme. But in other places, the diversity goes far beyond that genus. The heel proved to be the big fungal jungle, hosting around 80 different genera. Second and third place were won by the webbing between the toes and toenails. Fungi do love our feet. Intriguingly, the diversity of fungi and bacteria travel in opposite directions around our body. Feet have a low diversity of bacteria, while arms–dominated by the single genus Malassezia–have a rich variety of bacterial species. Fungi may have become especially adapted to feet because we can pick up spores on our soles. Our shoes then create wonderfully humid, airless habitats for them to grow.

Segre’s survey is, by design, only skin deep, and so it’s hardly the full fungal story. Writing this week in Trends in Microbiology, Gary Huffnagle of the University of Michigan and Mairi Noverr of Louisiana State University catalog the more preliminary expeditions inside our bodies. Our mouths cradle many species of fungi, although many of them are probably transients that wind up there riding on food or breaths. On the other hand, there are a number of species–in the mouth and elsewhere–that are specialized for life in various parts of our bodies. Some species can survive in the acid-drenched depths of our stomachs, for example.

Even Pneumocystis, Huffnagle and Noverr suggest, may actually be very well-adapted to life in humans. It has become so dependent on humans that it has lost the genes for building some essential compounds. Instead of being self-suffcient, it takes these compounds from us. As strange as it may sound, Pneumocystis may actually be a quiet lodger in our lungs most of the time. It goes unnoticed in healthy people because of its rarity, a rarity enforced by our immune system. Our immune system tolerates a few of the fungi, but if their numbers grow to large, it culls the herd. Only when HIV or some other disruption weakens the immune system does the balance collapse. Unchecked, Pneumocystis turns the lungs into a mushroom colony.

A similar disruption may explain other fungal disorders. Malassezia obviously can exist peacefully with our immune systems, given that it’s all over us. But in some cases, our immune system begins to look upon some of the proteins made by the fungus as a danger and responds with inflammation. Fungi can thus help give rise to allergies and immune disorders like eczema. (Dandruff is another result of a bad relationship with Malassezia, it turns out.)

Our resident bacteria may also help keep fungi in check. Scientists have found that a microbe-destroying course of antibiotics can raise the risk of a bloom of Candida fungi.a bloom of Candida fungi.a bloom of Candida fungi. It’s possible that the bacteria work against fungi simply by grabbing most of the good attachment points in our bodies. They may even spray their own anti-fungal drugs around their vicinity.

A big question for future generations of fungus surveyors will be whether the hundreds of species of fungi in our bodies do us any good at all. “There is no strong evidence for a mutualistic or beneficial relationship with the fungal microbiome,” Huffnagle and Noverr write. But this might just be the result of how little research scientists have done on the question. And there are some good reasons to explore the possibility. Some species of yeast show promise as probiotics against bacterial infections, for example. And we’re all intimately familiar with the alchemy of fungi–from bread to beer. Synthetic biologists are now using yeast’s versatility to make malaria drugs and biofuel. Long before biologists discovered fungal alchemy, cows were taking advantage of it to break down the plants they eat. Perhaps our own fungal garden is helping us out in ways we don’t yet understand.

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Photo by Dallas75, via Creative Commons.