A Foundation for the Oral Microbiome and Metagenome

描述（由申请人提供）：本研究的长期目标是表征人类口腔中存在的可培养和目前未培养的微生物（微生物组）及其所有基因（宏基因组），以便对健康和疾病中的宿主-微生物组相互作用进行综合研究。该项目的目的是确定未命名和未培养的口腔类群，并获得广泛的宏基因组序列信息，以代表这些微生物的系统发育多样性。最近的研究已经确定了口腔中的近800种，其中35%已命名，11%未命名但以菌株为代表，54%未命名且仅以16S rRNA序列的种型已知。目前还没有为未命名的65%的微生物组命名方案，因此几乎不可能将序列，表型，患病率，疾病关联和书目信息联系起来。目标1将通过命名未命名的种型，并为所有原核生物口腔类群建立一个可管理的、可访问互联网的人类口腔微生物组数据库，使这些重要类型的数据联系起来成为可能。口腔中有121个属的物种，其中一半属的基因组信息很少。目的2将获得105种人类口腔细菌的部分基因组序列。每个物种的基因组文库将被构建，每端384个克隆将被测序，每个物种的基因组覆盖率为10%-20%。这将为每个物种增加600个基因和蛋白质的信息，并为口腔宏基因组增加6万多个新的基因序列。这些系统发育多样性的序列将有助于在其他宏基因组项目中将contigs归为特定的属或种。目前，65%的口腔原核生物只知道基于16S rRNA序列的种型。有意义的生物学表征需要在实验台上操纵活的生物体。目标3将鉴定和存放大约200种未命名的口腔类群的参考菌株。从具有表型特征的研究者培养收集的菌株将通过16S rRNA序列分析和美国型培养收集的新参考菌株进行鉴定。这一建议将大大提高我们对人类微生物组的理解，并最终了解其与宿主在口腔健康和疾病中的相互作用。

DESCRIPTION (provided by applicant): The long-term objective of this research is to characterize the cultivable and currently uncultivated microorganisms present in the human oral cavity (microbiome) and all of their genes (metagenome) in order to develop an integrated view of host-microbiome interactions in health and disease. The objectives of this project are to define the unnamed and uncultured oral taxa and to obtain broad metagenomic sequence information that is representative of the phylogenetic diversity of these microorganisms. Recent studies have identified almost 800 species in the oral cavity, of which 35% are named, 11% unnamed but represented by strains, and 54% are unnamed and known only as 16S rRNA sequence phylotypes. There is currently no naming scheme for the unnamed 65% of the microbiome, thus it is nearly impossible to link sequence, phenotypic, prevalence, disease association, and bibliographic information. Aim 1 will make it possible to link these important types of data by naming the unnamed phylotypes, and establishing a curated, Internet-accessible Human Oral Microbiome Database for all prokaryotic oral taxa. There are species from 121 genera in the oral cavity and only minimal genomic information exists for half of these genera. Aim 2 will obtain partial genome sequences for 105 phylogenetically diverse human oral bacteria. Genomic libraries for each species will be constructed and 384 clones will be sequenced from each end, yielding 10%-20% genome coverage for each species. This will add information on 600 genes and proteins for each species and over 60,000 new gene sequences to the oral metagenome. These phylogenetically diverse sequences will facilitate attribution of contigs to specific genera or species in other metagenome projects. Currently, 65% of oral prokaryotes are known only as phylotypes based on 16S rRNA sequences. Meaningful biological characterization requires having living organisms to manipulate on the bench. Aim 3 will identify and deposit reference strains of approximately 200 unnamed oral phylotypes. Strains from phenotypically characterized investigator culture collections will be identified by 16S rRNA sequence analysis and novel reference strains deposited with the American Type Culture Collection. This proposal will significantly enhance our understanding of the human microbiome and allow eventual understanding of its interaction with the host in oral health and disease. This proposal is in response to PA-04-131, Metagenomic Analyses of the Oral Microbiome. This research will help us to understand the several hundred bacteria that live in the human oral cavity and their genes. These bacteria can cause tooth decay, periodontal disease, and infections elsewhere in the body. Knowing more about these many bacteria will allow scientists to develop better methods for treating and preventing oral diseases.