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Applied and Environmental Microbiology, August 2008, p. 4898-4909, Vol. 74, No. 15
0099-2240/08/$08.00+0     doi:10.1128/AEM.02884-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis{triangledown} ,{dagger}

Brian B. Oakley,1,{ddagger} Tina L. Fiedler,1 Jeanne M. Marrazzo,2 and David N. Fredricks1*

Program in Infectious Diseases, D3-100, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, Washington 98109-1024,1 Harborview Medical Center, 325 Ninth Avenue, Mailstop 359931, Seattle, Washington 981042

Received 20 December 2007/ Accepted 12 May 2008

Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 ± 0.7 versus 5.2 ± 0.75 (mean ± standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.

* Corresponding author. Mailing address: Program in Infectious Diseases, D3-100, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109-1024. Phone: (206) 667-6706. Fax: (206) 667-4411. E-mail: dfredric{at}fhcrc.org

{triangledown} Published ahead of print on 16 May 2008.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

{ddagger} Present address: Microbiology Research Group, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.

Applied and Environmental Microbiology, August 2008, p. 4898-4909, Vol. 74, No. 15
0099-2240/08/$08.00+0     doi:10.1128/AEM.02884-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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