Microbial ecology of the skin in the era of metagenomics and molecular microbiology

Abstract

The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

Figure 1.

The workflow of a bacterial 16S rRNA gene microbiome study. A heterogeneous mixture of genomic DNA is extracted from samples taken from the skin. Primers, containing barcodes that allow for multiplexing, are designed to the desired region of the 16S rRNA gene. 16S rRNA gene PCR products are amplified and sequenced. Low-quality sequences are removed, and various analyses are performed. These analyses can include assignment to taxonomy, analysis of shared phylogeny, and analysis of microbial community membership, structure, and diversity.

Figure 2.

Bacterial diversity of the skin. Phylogenetic tree of the domain Bacteria with each branch representing a phylum. Black branches represent numerically abundant phyla on the skin, red branches represent rare phyla on the skin, and green branches represent phyla that are absent from the skin. (The data are derived from Grice et al. 2009.)

Figure 3.

Changes in skin microbiota are associated with disease. (A) Relative abundance of bacteria (16S rRNA) in 12 children with AD flares as compared with 11 healthy controls (Kong et al. 2012). (B) Relative abundance of bacteria (16S rRNA) in six patients with psoriasis, in the lesional area as compared with unaffected skin as a control (Gao et al. 2008). (C) Relative abundance of P. acnes strains in 49 acne patients and 52 healthy individuals (Fitz-Gibbon et al. 2013). (D) Relative abundance of fungi (26S rRNA) in three healthy scalps and four dandruff-afflicted scalps (Park et al. 2012).