CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.
CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.
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DOI：
10.1371/journal.pone.0019051
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发表时间：
2011-04-22
期刊：
影响因子：
3.7
通讯作者：
Leys EJ
中科院分区：
文献类型：
--
作者：
Griffen AL;Beall CJ;Firestone ND;Gross EL;Difranco JM;Hardman JH;Vriesendorp B;Faust RA;Janies DA;Leys EJ
通过BLAST将细菌16 S rDNA序列与GenBank和其他大型公共数据库进行比较，通常提供的结果对于感兴趣的生物体的鉴定和分类分配几乎没有用处。人类微生物组，特别是口腔微生物组，包括许多分类群，准确识别序列数据对于这些群落的研究至关重要。为此，开发了核心口腔微生物组CORE的遗传学策划的16 S rDNA数据库。其目标是包括一个全面的和最小冗余的表示，经常居住在人类口腔中的细菌与计算强大的分类在物种和属的水平。栽培和未栽培类群的分支形成的基础上，使用多个标准，包括最大似然拓扑结构和引导支持，遗传距离，和以前的命名序列分析。以前命名的物种，特别是在属的水平上的一些分类不一致的问题得到了解决。将CORE数据库用于鉴定临床序列的性能与三个公开可用的数据库（GenBank nr/nt、RDP和HOMD）的性能进行比较，使用一组未用于创建数据库的测序读段。与其他公共数据库相比，CORE在通过多种标准识别人类口腔细菌16 S序列方面提供了更好的性能。此外，CORE数据库和系统发育树提供了一个框架的措施，社区分歧，和集中的大小的数据库提供了效率的优势，BLAST搜索的大数据集。CORE数据库可作为一个可搜索的界面，并可在http://microbiome.osu.edu下载。
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 support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.
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