A Foundation for the Oral Microbiome and Metagenome

描述（由申请人提供）：口腔研究团体的主要目标是了解微生物-微生物和微生物-宿主相互作用如何影响人类健康和疾病。拟议的研究将使研究界能够通过提供以下研究资源来实现这一目标：人类口腔微生物组数据库（HOMD），这是一个可通过网络访问的分类和基因组数据库，其中包括口腔分类描述和微生物组分析工具; 150种以前未培养的口腔细菌的参考菌株，以促进体内和体外实验;以及目前缺乏遗传信息的100个口腔分类群的基因组。第一个目标将提供和扩展口腔细菌的临时命名方案（分类法），包括那些尚未正式命名或培养的细菌。HOMD将扩展到描述超过1,000个人类口腔分类群，并将纳入人类微生物组项目对9个口腔部位进行深度16 S rRNA测序的结果。这一目标的完成将使研究人员能够将表型，临床，基因组和书目信息与基于16 S rRNA序列精确定义的口腔分类群联系起来。近三分之一的400个最普遍的口头类群没有已知的栽培隔离和第二个目标解决这个问题。这些分离株将通过研究者坦纳和韦德的培养物收集物以及L.五霍尔德曼摩尔和已故的艾德摩尔，弗吉尼亚理工学院，现在住在福赛斯研究所。不同门的目标分离物，如TM 7，Chlorobi，SR 1等，将在聚生体中生长，并在纯培养物中分离，如果可能的话，使用我们描述的方法。代表以前未培养物种的分离株将使研究人员能够研究体外生物膜生长，开发遗传系统，并进行动物模型实验。第三个目标将获得目前缺乏基因组信息的150个口腔分类群的基因组序列。它还将为口腔细菌提供宏基因组序列，这些细菌可以在聚生体中生长，但不能在纯培养物中生长。该项目将完成几乎所有400种最流行的口腔细菌的参考基因组的生产。这些信息将成为解释宏基因组数据、生产用于转录组研究的微阵列以及从基因组编码生成用于蛋白质组学研究的蛋白质片段文库的永久资源。该项目产生的基因组信息、工具和菌株将作为研究口腔微生物组在人类健康和疾病中作用的永久基础和资源。

DESCRIPTION (provided by applicant): A major goal of the oral research community is to understand how microbe-microbe and microbe- host interactions affect human health and disease. The proposed research will enable the research community to reach this goal by providing the following research resources: the Human Oral Microbiome Database (HOMD), a web accessible taxonomic and genomic database with oral taxon descriptions and microbiome analysis tools; reference strains for 150 previously uncultured oral bacteria to facilitate in vivo and in vitro experimentation; and genomes for 100 oral taxa that currently lack genetic information. The first Aim will provide and expand a provisional naming scheme (taxonomy) for oral bacteria, including those that have not been formally named or cultivated. HOMD will be expanded to describe over 1,000 human oral taxa, and will incorporate results from the Human Microbiome Projects deep 16S rRNA sequencing of nine oral cavity sites. Completion of this aim will allow investigators to link phenotypic, clinical, genomic and bibliographic information to precisely defined oral taxa based on 16S rRNA sequences. Nearly one-third of the 400 most prevalent oral taxa have no known cultivated isolate and the Second Aim addresses this issue. Such isolates will be identified by 16S rRNA sequencing from the culture collections of investigators Tanner and Wade, and from the collection of L. V. Holdeman Moore and the late Ed Moore, Virginia Polytechnic Institute, now housed at The Forsyth Institute. Targeted isolates for diverse phyla such as TM7, Chlorobi, SR1 and others will be grown in consortia and isolated in pure culture, where possible, using methods we have described. Isolates representing previously uncultivated species will allow investigators to study of in vitro biofilm growth, develop genetic systems, and perform animal model experiments. The Third Aim will obtain genome sequences for 150 oral taxa currently lacking genome information. It will also provide metagenome sequences for oral bacteria that can grow in consortia but not in pure culture. This project will complete the production of reference genomes for nearly all the 400 most prevalent oral bacteria. This information will be a permanent resource for interpretation of metagenome data, for the production of microarrays for transcriptome studies, and for generating protein fragment libraries from genomic coding for proteomic studies. The genome information, tool, and strains generated by this project will serve as a permanent foundation and resource for investigations on the role of the oral microbiome in human health and disease.