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NIH Team Presents Findings from Fungi-focused Study of Skin Microbiome

NEW YORK (GenomeWeb News) – The foot is home to some of the most diverse and variable fungal communities on the human body, a new skin microbiome study suggests.

"[Y]our feet are teeming with fungal diversity, so wear your flip flops in locker rooms if you don’t want to mix your foot fungi with someone else’s fungi," the National Human Genome Research Institute's Julie Segre, co-senior author on the study, said in a statement.

Together with Heidi Kong, a dermatology researcher at the National Cancer Institute, Segre led a group of NHGRI and NCI researchers who performed 18S ribosomal RNA sequencing, internal transcribed spacer sequencing, and 16S rRNA gene sequencing on skin swab samples from 10 individuals in their quest to characterize fungal and bacterial communities at more than a dozen sites across the human body.

As they reported online today in Nature, analyses of these sequences indicated that fungi from a single genus tend to be prevalent at most of the skin sites tested, though samples from three areas on the foot generally had far more elaborate fungal communities.

The ongoing effort to catalog and characterize the microbes living in and on the human body has produced reams of data related to the bacterial representatives in these microbiomes. But to date there has been more limited research looking at fungal contributors to these communities. Moreover, study authors noted, past studies of fungal disease have primarily relied on culture-based approaches that overlook tricky-to-culture fungi.

"By gaining a more complete awareness of the fungal and bacterial ecosystems, we can better address associated skin diseases, including skin conditions [that] can be related to cancer treatments," NCI's Kong said in a statement.

With that in mind, the researchers compared culture and genetics-based approaches to characterizing fungi on the human skin.

For their genetic analysis, they used two main DNA markers to try to better define fungal members of human microbial communities: sequences from the fungal 18S rRNA gene and from the neighboring internal transcribed spacer 1 region.

The team did Roche 454 GS20/FLX Titanium sequencing on 18S and ITS1 amplicons generated for samples from 10 seemingly healthy individuals between 18- and 40-years-old, focusing on 14 body sites per person.

For their follow-up analyses, investigators also folded in 16S rRNA gene sequence information to get a glimpse at the bacterial species present in the skin swab samples.

The newly generated 18S and ITS1 amplicon sequence data identified far more fungal representatives than could be detected by traditional culturing methods, study authors noted, including fungi from both the Ascomycetes and Basidiomycetes phyla.

"DNA sequencing reveals the great diversity of fungi, even those that are hard to grow in culture," Segre said, adding that "DNA sequencing enabled us to learn immeasurably more about where fungi predominate as a part of the human skin microbiome."

In some cases, samples from the healthy individuals contained fungi from genera that have been linked to disease in those with compromised immunity, such as Candida. At 11 of the main body, arm, face, and ear sites tested, though, researchers saw a marked over-representation of species belonging to a single genus, called Malassezia.

"[W]e identified 11 of the 14 known Malassezia species among skin sites," study authors noted, "suggesting that human skin is colonized with a wide range of Malassezia."

"Based on species-level resolution," they added, "we observed that fungal diversity is more dependent on body site than individual subject."

Still, the limited fungal variety found at most sites in the body belied the extensive diversity that the group saw when it looked at fungal communities from human foot sites.

There, researchers uncovered extensive diversity both within and between study participant samples. Fungal communities from the bottom of the heel were especially diverse, they reported, harboring a median of around 80 fungal genera per person.

By folding in information on the bacterial species present at the sites tested, meanwhile, the group found that foot areas with high fungal diversity tend to have lower bacterial diversity. At some arm and body sites, on the other hand, that relationship was more or less reversed. And still other body sites appeared to have low fungal and bacterial diversity within their microbiomes.

"This systematic study clearly demonstrates that human skin surfaces are complex ecosystems, providing diverse environments for microorganisms that inhabit our bodies," the team noted.

"Different factors determine the bacterial and fungal communities," they added, "depending on the physiological properties of the skin."

Going forward, the information gleaned from the new skin microbiome study and others like it is expected to help researchers better understand which fungi are beneficial to human health and which are detrimental — as well as the circumstances influencing such relationships.

As such, those involved in the current analyses argued that the findings "provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintenance of human health and to disease pathogenesis."

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