The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
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DOI：
10.1093/database/baq013
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发表时间：
2010-07-06
期刊：
影响因子：
--
通讯作者：
Dewhirst FE
中科院分区：
文献类型：
--
作者：
Chen T;Yu WH;Izard J;Baranova OV;Lakshmanan A;Dewhirst FE
人类口腔微生物组是研究最多的人类微生物区系，但53%的物种尚未被有效命名，35%仍处于未培养状态。未栽培的分类群主要从16 S rRNA序列信息中已知。序列信息仅与模糊的分离株或克隆编号相关，并且通常缺乏准确的系统发育位置，这是使用人类口腔微生物组数据的主要障碍。创建人类口腔微生物组数据库（HOMD）的目标是为科学界提供一个身体部位特异性的综合数据库，该数据库基于一个基于16 S rRNA基因的临时命名方案，涵盖人类口腔中存在的600多种原核生物物种。目前，HOMD提供两种主要类型的信息-分类和基因组。命名的口腔物种和分类群从口腔分离株的16 S rRNA基因序列分析和克隆研究中确定的被放置到定义的16 S rRNA基因组类型和每个给定的独特的人类口腔分类群（HOT）编号。HOT链接了每个分类单元的表型、系统发育、基因组、临床和书目信息，提供了一个BLAST搜索工具，用于将用户16 S rRNA基因序列与一个精选的全长16 S rRNA基因参考数据集进行匹配。对于基因组分析，HOMD提供了一套全面的分析工具，并为所有已测序和公开发布的人类口腔微生物基因组维护经常更新的注释。口腔细菌基因组序列，作为人类微生物组计划的一部分，正在被添加到HOMD，因为他们变得可用。我们提供HOMD作为展示其他人体部位微生物组数据的概念模型。数据库URL：http://www.homd.org
The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org
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