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The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

机译：人类口腔微生物组数据库：一种可访问网络的资源，用于研究口腔微生物的分类学和基因组信息

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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
机译：人类口腔微生物组是研究最多的人类微生物区系，但尚未有效命名该物种的53％，还有35％尚未培养。主要从16S rRNA序列信息中得知未培养的分类单元。仅与模糊的分离物或克隆编号相关的序列信息，通常缺乏准确的系统发生位置，是处理人类口腔微生物组数据的主要障碍。建立人类口腔微生物组数据库（HOMD）的目的是为科学界提供基于特定16S rRNA基因的人类口腔中存在的600多种原核生物物种的特定于身体部位的综合数据库临时命名方案。当前，HOMD提供了两种主要类型的信息：分类信息和基因信息。通过对口腔分离株的16S rRNA基因序列分析和克隆研究鉴定出的命名的口腔物种和分类群，放入定义的16S rRNA系统型中，并分别赋予唯一的人类口腔分类群（HOT）编号。 HOT链接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，可将用户16S rRNA基因序列与指定的全长16S 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，并为已测序并公开发布的所有人类口腔微生物基因组维护了经常更新的注释。作为人类微生物组计划的一部分确定的口腔细菌基因组序列，将在其可用时添加到HOMD中。我们提供HOMD作为表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

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