core a phylogenetically-curated 16s rdna database of the core oral microbiome的核心phylogenetically-curated 16 s rdna数据库核心口腔微生物.pdfVIP

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome 1 2 2 1 1 Ann L. Griffen *, Clifford J. Beall , Noah D. Firestone , Erin L. Gross , James M. DiFranco , Jori H. 3 2¤a 2¤b 3 2 Hardman , Bastienne Vriesendorp , Russell A. Faust , Daniel A. Janies , Eugene J. Leys 1 Division of Pediatric Dentistry, College of Dentistry, The Ohio State University, Columbus, Ohio, United States of America, 2 Division of Oral Biology, College of Dentistry, The Ohio State University, Columbus, Ohio, United States of America, 3 Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America Abstract Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum- likelihood-based topology and bootstrap s