Topographic diversity of fungal and bacterial communities in human skin
Open accessAbstract
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 microbiota. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also have major roles in microbial community stability, human health and disease. Genomic methodologies to identify fungal species and communities have been limited compared with those that are available for bacteria. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes. 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.
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Skin samples enriched for Malassezia species, including M. globosa, M. furfur, M. restricta, and M. arunalokei, which dominate the healthy human skin mycobiome, were rarely positive for C. auris.
“Skin samples enriched for Malassezia species, including M. globosa, M. furfur, M. restricta, and M. arunalokei, which dominate the healthy human skin mycobiome, were rarely positive for C. auris [12,69].”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [69]
The Human Skin Fungal Diversity section reports that Malassezia predominated at eleven skin sites in healthy volunteers, with M. restricta and M. globosa predominant at particular sites. It does not establish that all four named species dominate healthy skin; its species list does not include M. arunalokei. The paper also does not report whether Malassezia-enriched samples were positive for C. auris. (LLM, conf=0.88)
Experimental — accuracy not yet measuredSkin microbial communities can restrict bacterial pathogens through metabolic competition and immune modulation.
“Since skin microbial communities can restrict bacterial pathogens through metabolic competition and immune modulation [69–72]”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [69]
The discussion in our copy says microbial community instability may give potentially pathogenic microbes an opportunity to establish disease, but it does not say that skin communities restrict bacterial pathogens. Its mention of immune effects concerns fungal commensals in intestinal disease. Searches for metabolic competition and immune modulation found no passage establishing either proposed mechanism on skin. (LLM, conf=0.72)
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- Authors
- NIH Intramural Sequencing Center Comparative Sequencing Program, Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., Schoenfeld, D., Nomicos, E., Park, M., Kong, H. H., & Segre, J. A.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Kong, Heidi H.
- Segre, Julia A.
- Venue
- Nature
- Published
- 2013-05-22
- Volume
- 498
- Issue
- 7454
- Pages
- 367-370
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3711185
- OpenAlex
- W2074335138
- Cited by
- 1,206
- References
- 42
- Citations by year
- 2026: 73 · 2025: 92 · 2024: 111 · 2023: 89 · 2022: 103 · 2021: 107 · 2020: 133 · 2019: 105 · 2018: 73 · 2017: 89 · 2016: 76 · 2015: 70 · 2014: 60 · 2013: 23
- FWCI
- 50.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (ZIAHG000180)
- National Cancer Institute (ZIABC010938)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (4UH3 AR057504-02, 1UH2AR057504-01, 1K99AR059222)
- Topics
- Health Sciences › Medicine › Epidemiology › Nail Diseases and Treatments
- Health Sciences › Medicine › Dermatology › Dermatology and Skin Diseases
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- skin microbiome, fungal communities, bacterial communities, Malassezia, skin topography, tinea pedis, toenail infection, microbial community stability, commensal microbiota, fungal diversity
- MeSH terms
- Adult, Bacteria, District of Columbia, Female, Fungi, Health, Homeostasis, Humans, Malassezia, Male, Molecular Sequence Data, Skin, Databases, Genetic, Biodiversity, Young Adult
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