A Foundation for the Oral Microbiome and Metagenome

口腔微生物组和宏基因组的基础

基本信息

批准号：
9898161
负责人：
Floyd E Dewhirst
金额：
$ 91.8万
依托单位：
ADA FORSYTH INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-04-01 至 2022-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9898161
关键词：
16S ribosomal RNA sequencing Access to Information Address Adopted Affect Animal Model Bacteria Bibliography Biochemical Biological Chlorobi Chloroflexi Clinical Code Collection Communities DNA Data Databases Dental caries Diagnosis Disease Foundations Funding Genetic Genome Genomic Library Genomics Goals Growth Health Health Professional Heart Diseases Human Human Microbiome Human Resources In Vitro Institutes Investigation Knowledge Link Methods Microbe Microbial Biofilms Mouth Diseases Names National Institute of Dental and Craniofacial Research Oral Oral cavity Oral health Organism Outcome Pathogenicity Phenotype Play Positioning Attribute Premature Birth Production Protein Fragment Proteomics Research Research Personnel Resources Ribosomal RNA Role Scheme Scientist Site Stroke System Taxon Taxonomy Virginia analytical tool base cost experimental study genetic information genetic makeup host-microbe interactions in vivo member metagenome microbial microbial host microbiome microbiome analysis microbiome components novel online resource oral bacteria oral microbiome prevent public health relevance reference genome tool transcriptome web-accessible

项目摘要

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.

描述（由申请人提供）：口头研究界的主要目标是了解微生物和微生物的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），这是一个可访问的网络分类学和基因组数据库，该数据库具有口腔分类单元描述和微生物组分析工具； 150种先前未培养的口服细菌的参考菌株，可促进体内和体外实验；目前缺乏遗传信息的100个口腔类群的基因组。第一个目的将为口腔细菌提供并扩展一个临时命名计划（分类法），包括尚未正式命名或培养的细菌。 HOMD将扩展以描述1000多个人类口腔分类单元，并将结合人类微生物组项目的结果，深16S rRNA测序，对9个口腔场地进行了测序。此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16S rRNA序列精确定义的口腔分类单元联系起来。在400个最普遍的口腔群中，将近三分之一没有已知的栽培分离株，第二个目的解决了这个问题。这种分离株将通过研究人员Tanner和Wade的培养物收集的16S rRNA测序，以及从L. V. Holdeman Moore和已故的Ed Moore收集的弗吉尼亚州理工学院，现在位于福赛斯研究所。用于TM7，Chlorobi，Sr1等多种门的靶向分离株将使用我们描述的方法在纯培养中生长，并在纯培养中分离。代表以前未经文化的物种的分离株将使研究人员能够研究体外生物膜生长，发展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个口腔类群的基因组序列。它还将为可以在财团中生长但不能在纯文化中生长的口腔细菌提供元基因组序列。该项目将完成几乎所有400个最普遍的口服细菌的参考基因组的产生。该信息将是解释元基因组数据，用于转录组研究的微阵列以及从基因组编码蛋白质组学研究中生成蛋白质片段文库的永久资源。该项目产生的基因组信息，工具和菌株将成为对口腔微生物组在人类健康和疾病中的作用进行调查的永久基础和资源。