Findley K, Oh J, Yang J et al.Topographic diversity of fungal and bacterial communities in human skin. Nature 498:367-370

Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Nature (Impact Factor: 41.46). 05/2013; 498(7454). DOI: 10.1038/nature12171
Source: PubMed


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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    • "Fewer than 10% of the cells in our bodies are actually our own. Most of these organisms are bacteria, but we are also colonized by multicellular species including fungi [1], intestinal worms [2] and ectoparasites, such as lice [3]–[5], with nearly 2000 pathogen and parasite species alone known from human bodies [6]. Among the more enigmatic of the multicellular species that live on humans, as well as on other mammals, are mites of the genus Demodex (reviewed in [7]), which are common on human faces and other parts of the body [8], [9]. "
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    ABSTRACT: Demodex mites are a group of hair follicle and sebaceous gland-dwelling species. The species of these mites found on humans are arguably the animals with which we have the most intimate interactions. Yet, their prevalence and diversity have been poorly explored. Here we use a new molecular method to assess the occurrence of Demodex mites on humans. In addition, we use the 18S rRNA gene (18S rDNA) to assess the genetic diversity and evolutionary history of Demodex lineages. Within our samples, 100% of people over 18 years of age appear to host at least one Demodex species, suggesting that Demodex mites may be universal associates of adult humans. A phylogenetic analysis of 18S rDNA reveals intraspecific structure within one of the two named human-associated Demodex species, D. brevis. The D. brevis clade is geographically structured, suggesting that new lineages are likely to be discovered as humans from additional geographic regions are sampled.
    PLoS ONE 08/2014; 9(8):e106265. DOI:10.1371/journal.pone.0106265 · 3.23 Impact Factor
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    • "This was observed for all sample types with the exception of nasal samples from healthy control individuals (Figure 2), and is consistent with nasal fungal analysis in the nares [26]. However, the genus Malassezia was not predominant in this study, as has been reported previously for diverse skin sites, probably due to different environmental conditions of the body sites sampled [26]. Again, communities clustered according to sample type (oropharynx, nasal, and sputum) (Figure 2), and TB patient sputum and oropharynx samples showed similar relative abundances with no significant differences at the phylum level (Figure 2, Table 3). "
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    ABSTRACT: Background Changes in respiratory tract microbiota have been associated with diseases such as tuberculosis, a global public health problem that affects millions of people each year. This pilot study was carried out using sputum, oropharynx, and nasal respiratory tract samples collected from patients with pulmonary tuberculosis and healthy control individuals, in order to compare sample types and their usefulness in assessing changes in bacterial and fungal communities. Findings Most V1-V2 16S rRNA gene sequences belonged to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with differences in relative abundances and in specific taxa associated with each sample type. Most fungal ITS1 sequences were classified as Ascomycota and Basidiomycota, but abundances differed for the different samples. Bacterial and fungal community structures in oropharynx and sputum samples were similar to one another, as indicated by several beta diversity analyses, and both differed from nasal samples. The only difference between patient and control microbiota was found in oropharynx samples for both bacteria and fungi. Bacterial diversity was greater in sputum samples, while fungal diversity was greater in nasal samples. Conclusions Respiratory tract microbial communities were similar in terms of the major phyla identified, yet they varied in terms of relative abundances and diversity indexes. Oropharynx communities varied with respect to health status and resembled those in sputum samples, which are collected from tuberculosis patients only due to the difficulty in obtaining sputum from healthy individuals, suggesting that oropharynx samples can be used to analyze community structure alterations associated with tuberculosis.
    08/2014; 2(1):29. DOI:10.1186/2049-2618-2-29
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    • "Fungi, viruses, and mites also contribute to the human skin microbiome. The first large-scale sequencing analysis characterized fungal ( " mycobiome " ) diversity on the skin of 10 healthy adult volunteers (HVs) (Findley et al. 2013). A total of 14 skin sites representing a range of physiological characteristics—dry , moist, and oily—were sampled via the swab method. "
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    ABSTRACT: Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms.
    Cold Spring Harbor Perspectives in Medicine 08/2014; 4(8). DOI:10.1101/cshperspect.a019802 · 9.47 Impact Factor
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