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dc.contributor.authorFettweis, Jennifer Men_US
dc.contributor.authorSerrano, Myrna Gen_US
dc.contributor.authorSheth, Nihar Uen_US
dc.contributor.authorMayer, Carly Men_US
dc.contributor.authorGlascock, Abigail Len_US
dc.contributor.authorBrooks, J Paulen_US
dc.contributor.authorJefferson, Kimberly Ken_US
dc.contributor.authorVaginal Microbiome Consortium (additional members)en_US
dc.contributor.authorBuck, Gregory Aen_US
dc.date.accessioned2012-12-17T16:08:33Z
dc.date.available2012-12-17T16:08:33Z
dc.date.issued2012-12-17
dc.identifier.citationBMC Genomics. 2012 Dec 17;13(Suppl 8):S17en_US
dc.identifier.urihttp://hdl.handle.net/10919/19093
dc.description.abstractBackground The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. Results We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. Conclusions This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.en_US
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCreative Commons Attribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleSpecies-level classification of the vaginal microbiomeen_US
dc.typeArticle - Refereed
dc.date.updated2012-12-17T16:08:33Z
dc.description.versionPeer Reviewed
dc.rights.holderJennifer M Fettweis et al.; licensee BioMed Central Ltd.en_US
dc.title.serialBMC Genomics
dc.identifier.doihttps://doi.org/10.1186/1471-2164-13-S8-S17
dc.type.dcmitypeText


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Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International