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More Fungi than a Barrel of Monkeys

Diana Gitig, Ph.D.

In the world of human microbes, bacteria have been getting all the attention. But now it’s time for fungi to get their share of the spotlight. Read more...

The human microbiome—generally defined as the enormous population of bacteria sharing our bodies, particularly on our skin and in our guts—has become very popular lately, even scoring the latest cover of The New York Times Magazine. But Heidi Kong, an Investigator in the Dermatology Branch of the National Cancer Institute (NCI), is quick to point out that microbial diversity is not limited to bacteria. We’ve got fungi living on our skin too—the "mycobiome," if you will—and like our bacterial stowaways, they can impact our health in a big way.

Fungi (cyan) is surrounded by a human hair (yellow) within the skin. Source: Alex Valm, PhD

Because fungi are known to be associated with a number of different skin conditions, Kong and colleagues sequenced the fungal populations on the skin of 10 healthy volunteers, as reported in this week’s Nature (1). They took samples from 14 different places on the volunteers’ bodies, including the face, chest, arms, ears, nostrils, head, and feet.

One genus of fungus, Malassezia, predominated, with different Malassezia species found at different sites. Fungal diversity, it turns out, depends more on the site of the body than on the individual. The highest fungal diversity, about 40–80 genera, was found on the feet, including the heel, the toenail, and the spaces between the toes, sites notorious for fungal infections such as athlete’s foot and nail fungus. Over a period of three months, these populations remained fairly consistent.

Fungal cell walls are more difficult to break down than bacterial cell walls, so the group had to develop new methods to extract the DNA for sequencing. “We also used a unique region of the fungal genome, the internal transcribed spacer 1 (ITS1) region, as a molecular tag to identify the different fungal species,” said Kong. “And since fungal databases are not as robust as those for bacteria, we first had to culture and sequence the different species in the lab to generate our own reference database.”

Overall, the team found no linear correlation between bacterial and fungal richness at the different skin sites, suggesting that different factors affect the two communities of microbes. Whereas fungal diversity was determined by locations on the skin, bacteria tended to be grouped according to the underlying physiology—for example, whether the skin was moist, dry, or sebaceous.

The study was made possible by recent advances in sequencing technologies, particularly metagenomic shotgun sequencing, which have the ability to sequence the DNA of a complex population, without identifying, or even knowing, its constituent members beforehand. Kong believes that the primary lesson learned from studies of the microbiome is that understanding the whole of the microbe population is vital; by parsing it into individual components, we will never be able understand, reconstruct, or repair the gestalt. Kong is taking this lesson to heart by making sure that all of our microbial partners—fungi and bacteria alike—get the attention they are due.


  1. Findley, K., J. Oh, J. Yang, S. Conlan, C. Deming, J. A. Meyer, D. Schoenfeld, E. Nomicos, M. Park, H. H. Kong, and J. A. Segre. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature advance online publication (May).