Molecular analysis of human forearm superficial skin bacterial biota

doi:10.1073/pnas.0607077104

Molecular analysis of human forearm superficial skin bacterial biota

Departments of *Medicine,
^†Environmental Medicine,
^‡Pathology, and
^¶Microbiology, New York University School of Medicine, New York, NY 10016; and
^§New York Harbor Veterans Affairs Medical Center, New York, NY 10010

Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved December 20, 2006 (received for review August 15, 2006)

Abstract

The microbial ecology of human skin is complex, but little is known about its species composition. We examined the diversity of the skin biota from the superficial volar left and right forearms in six healthy subjects using broad-range small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones. For the initial 1,221 clones analyzed, 182 species-level operational taxonomic units (SLOTUs) belonging to eight phyla were identified, estimated as 74.0% [95% confidence interval (C.I.), ≈64.8–77.9%] of the SLOTUs in this ecosystem; 48.0 ± 12.2 SLOTUs were found in each subject. Three phyla (Actinobacteria, Firmicutes, and Proteobacteria) accounted for 94.6% of the clones. Most (85.3%) of the bacterial sequences corresponded to known and cultivated species, but 98 (8.0%) clones, comprising 30 phylotypes, had <97% similarity to prior database sequences. Only 6 (6.6%) of the 91 genera and 4 (2.2%) of the 182 SLOTUs, respectively, were found in all six subjects. Analysis of 817 clones obtained 8–10 months later from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numbering 65). Only four (3.4%) of the 119 genera (Propionibacteria, Corynebacteria, Staphylococcus, and Streptococcus) were observed in each subject tested twice, but these genera represented 54.4% of all clones. These results show that the bacterial biota in normal superficial skin is highly diverse, with few well conserved and well represented genera, but otherwise low-level interpersonal consensus.

Footnotes

^‖To whom correspondence should be addressed. E-mail: martin.blaser{at}med.nyu.edu
Author contributions: Z.G., Z.P., and M.J.B. designed research; Z.G. performed research; Z.G., C.-h.T., Z.P., and M.J.B. analyzed data; and Z.G. and M.J.B. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS direct submission.
Data deposition: The 16S rDNA sequences of clones representing previously uncharacterized phylotypes as defined in this study have been deposited in the GenBank database (accession nos. DQ130020–DQ130049 and DQ847437–DQ847450).
This article contains supporting information online at www.pnas.org/cgi/content/full/0607077104/DC1.
Abbreviations:

SLOTU,

species-level operational taxonomic unit;

RDP,

Ribosomal Database Project;

C.I.,

confidence interval;

DPCoA,

double principal coordinate analysis;

16S rDNA,

small subunit rRNA genes.