Topographic diversity of fungal and bacterial communities in human skin

Microbial sequencing of samples obtained from multiple skin sites in healthy human adults shows that core-body and arm sites are dominated by fungal species of the genus Malassezia, whereas foot sites show high fungal diversity, and that skin topography is associated with differential compositions of bacterial and fungal communities. As well as protecting against invasion by pathogens, our skin plays host to a varied population of microbes, some of which have important roles in human health and disease. The bacterial component of these communities is by now fairly well known, but our knowledge of the fungal members of the skin microbiota remains limited. Here Julia Segre and colleagues construct a map of the fungal species diversity at 14 different skin sites from 10 healthy adults, and compare this with the bacterial flora. They find that fungal richness varies across the body, and that bacterial and fungal communities are shaped by different factors. One finding with particular relevance to disease is that microbial communities around the feet that are commonly affected by fungal disease, such as athlete's foot, tend to be unstable. This instability may provide opportunities for harmful microbes to flourish. This finding highlights the need to develop new treatment strategies that specifically target microbial imbalances. Traditional culture-based methods have incompletely defined the microbial landscape of common recalcitrant human fungal skin diseases, including athlete’s foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms and provides a home for diverse commensal microbiota1. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders2,3,4. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also have major roles in microbial community stability, human health and disease5. Genomic methodologies to identify fungal species and communities have been limited compared with those that are available for bacteria6. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes7. Here we sequenced and analysed fungal communities of 14 skin sites in 10 healthy adults. Eleven core-body and arm sites were dominated by fungi of the genus Malassezia, with only species-level classifications revealing fungal-community composition differences between sites. By contrast, three foot sites—plantar heel, toenail and toe web—showed high fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that physiologic attributes and topography of skin differentially shape these two microbial communities. These results provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintainenace of human health and to disease pathogenesis.