Gene Sequencing Reveals Feet Have Greatest Fungal Diversity

Jenni Laidman

May 22, 2013

Human feet are fungal forests, the most diverse fungal ecosystem on the body, with some 80 separate genera represented, according to results from the first study of fungal diversity on healthy human skin.

Keisha Findley, PhD, postdoctoral fellow, National Human Genome Research Institute, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland, and colleagues published the survey of skin fungi online May 22 in Nature.

The researchers sequenced and analyzed the fungal communities from 14 skin sites in 10 healthy adults, using genetic material isolated from clinical swabs and amplified by polymerase chain reaction. The researchers relied on more than 5 million sequences of the intervening internal transcribed spacer 1 region between subunit rRNA genes to classify fungal diversity to species level.

Fungi identified in the study fell into 2 phyla, Ascomycetes and Basidiomycetes.

The researchers found that feet were home to the most fungal genera. The plantar heel (heel bottom) showed the most complex fungal community on the body, exhibiting a median richness among samples of some 80 genera. The toe web (between the third and fourth toe) was home to some 60 genera, and toenail swabs showed approximately 40 genera. The trunk and head showed the lowest fungal diversity, with about 10 genera present.

Hands, which have shown the richest bacterial diversity among body sites, were dominated by a single fungal genus, Malassezia, as were the core-body, head, and arm sites: the antecubital fossa (inner forearm), back, external auditory canal (ear), glabella (between the eyes), inguinal crease (skin fold between hip and groin), manubrium (upper sternum), nare (nostril), occiput (back of head), retroauricular crease (behind the ear), and volar forearm (wrist).

A species analysis, which identified approximately 80% to 90% of Malassezia species per skin site, showed certain fungal species associated with certain sites. For instance, M restricta predominated in the ear, behind the ear, and between the eyes, whereas M globosa was most populous at the back, occiput, and inguinal crease.

Some 29 million people in North America have fungal infections, but such infections can be difficult to treat, and the fungi involved can be difficult to identify. Before genetic sequencing, the identity of any fungus could only be determined via culturing, a time-consuming and often unsuccessful process. In this study, researchers also cultured parallel samples from 4 skin sites on healthy adult volunteers, successfully growing 130 fungal isolates representing 18 genera. In contrast, genetic sequencing revealed more than 80 genera.

"DNA sequencing reveals the great diversity of fungi, even those that are hard to grow in culture," coauthor Julie Segre, PhD, also from the National Human Genome Research Institute, in a National Institutes of Health news release. "DNA sequencing enabled us to learn immeasurably more about where fungi predominate as a part of the human skin microbiome."

The research showed that fungal species diversity correlated to the body site, not to the person, and that fungal community structure was the same on both sides of the body.

"The data from our study gives us a baseline about normal individuals that we never had before," Dr. Segre said in the release. "The bottom line is your 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 authors have disclosed no relevant financial relationships.

Nature. Published online May 22, 2013. Abstract

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