A diversity profile of the human skin microbiota

Abstract

The many layers and structures of the skin serve as elaborate hosts to microbes, including a diversity of commensal and pathogenic bacteria that contribute to both human health and disease. To determine the complexity and identity of the microbes inhabiting the skin, we sequenced bacterial 16S small-subunit ribosomal RNA genes isolated from the inner elbow of five healthy human subjects. This analysis revealed 113 operational taxonomic units (OTUs; "phylotypes") at the level of 97% similarity that belong to six bacterial divisions. To survey all depths of the skin, we sampled using three methods: swab, scrape, and punch biopsy. Proteobacteria dominated the skin microbiota at all depths of sampling. Interpersonal variation is approximately equal to intrapersonal variation when considering bacterial community membership and structure. Finally, we report strong similarities in the complexity and identity of mouse and human skin microbiota. This study of healthy human skin microbiota will serve to direct future research addressing the role of skin microbiota in health and disease, and metagenomic projects addressing the complex physiological interactions between the skin and the microbes that inhabit this environment.

Figure 1.

A cross-section of the skin and the regions sampled by each collection method.

Figure 2.

Phylogenetic architecture and abundance of OTUs with ≥97% similarity in five human subjects. The left axis is a neighbor-joining tree composed of representative sequences from each of the 113 OTUs identified in the subjects. Abundance of OTUs in each subject is indicated by a grayscale value in the heat plot to the right. Each column of the heat plot corresponds to each arm of the five subjects (L is left arm; R is right arm). The heat plot is color-coded according to the major bacterial divisions observed: Proteobacteria (red), Bacteroidetes (blue), Firmicutes (yellow), and Actinobacteria (green).

Figure 3.

A Venn diagram that illustrates observed overlap of OTUs with ≥97% similarity according to sampling method. Among the five subjects, a total of 113 OTUs were detected. Thirty-six OTUs were detected by all three sampling methods; 5225 sequences of the total 5373 sequences fall within these 36 overlapping OTUs (97.2%). J_abund and θ estimates of OTU community structure and membership along with standard errors (SEs) are reported in the accompanying table.

Figure 4.

Interpersonal and intrapersonal variation. A UPGMA dendogram of pairwise θ values comparing community structure of OTUs from each arm of each subject. The length of the scale bar represents a distance of 0.10 (1 − θ). Values for θ were calculated for OTUs with ≥97% similarity (Supplemental Table 3). (L) Left arm; (R) right arm.

Figure 5.

Comparison of relative abundance of bacteria in mouse ear punch and human punch biopsy libraries. 16S rDNA sequences are first grouped into division. Each division bar is then further broken down into class. When a particular genus dominated the class, the genus is noted. (hum) Human; (mus) mouse.