A Foundation for the Oral Microbiome and Metagenome

口腔微生物组和宏基因组的基础

• 批准号: 7585799
• 负责人: Floyd E Dewhirst
• 金额: $ 74.53万
• 依托单位: ADA FORSYTH INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-04-01 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7585799
• 关键词: Actinobacillus actinomycetemcomitans; American Type Culture Collection; Animal Model; Appointment; Bacteria; Bibliography; Biochemical; Biological; Blast Cell; Brain; Clinical; Collection; Communicable Diseases; Communities; Computer Simulation; Data; Databases; Dental; Dental caries; Deposition; Disease; Disease Association; Ear; Environment; Faculty; Family; Foundations; Genbank; Gene Proteins; Genes; Genetic; Genome; Genomic Library; Genomics; Goals; Habitats; Health; Heart; Host Defense Mechanism; Human; Human Microbiome; Infection; Infectious Diseases Research; Institutes; Institution; Internet; Investigation; Joints; Knowledge; Laboratories; Lead; Libraries; Life; Link; Liver; Lung; Medicine; Metagenomics; Methods; Microbe; Microbiology; Molecular; Molecular Analysis; Mouth Diseases; NIH Program Announcements; Names; National Institute of Dental and Craniofacial Research; Nucleic Acids; Online Systems; Oral; Oral cavity; Oral health; Organism; Pathologic; Periodontal Diseases; Phylogenetic Analysis; Porphyromonas gingivalis; Prevalence; Principal Investigator; Prokaryotic Cells; Proteins; Proteobacteria; PubMed; Publications; Qualifying; Research; Research Personnel; Resources; Ribosomal RNA; Scheme; Scientist; Sequence Analysis; Side; Site; Streptococcus mutans; Surveys; Systemic infection; Taxon; Taxonomy; Trees; United States; base; bone; cost; experience; genome sequencing; innovation; member; metagenomic sequencing; microbial; microbiome; microorganism; novel; oral bacteria; oral infection; oral microbiome; prevent; programs; research study; response; tool; vector

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.

这项研究的长期目的是表征可耕种且目前尚未进行的。 人口腔中存在的微生物（微生物组）及其所有基因（元基因组） 开发健康和疾病中宿主微生物组相互作用的综合观点。目标的目标 项目将定义未命名和未培养的口服分类单元，并获得广泛的宏基因组序列 代表这些微生物的系统发育多样性的信息。最近的研究 在口腔中已经确定了近800种，其中35％的命名为11％，但 由菌株表示，54％未命名，仅称为16S rRNA序列系统型。有 目前尚无针对微生物组的65％的未命名计划，因此几乎不可能链接 序列，表型，患病率，疾病关联和书目信息。 AIM 1会做到这一点 通过命名未命名的系统型并建立一个 为所有原核生物口腔分类群而策划的，互联网可访问的人口腔微生物组数据库。有 从口腔中的121属物种，仅存在最小的基因组信息。 属。 AIM 2将获得105种系统发育多样的人口腔细菌的部分基因组序列。 将构建每个物种的基因组文库，并从两端测序384个克隆， 每种物种产生10％-20％的基因组覆盖率。这将添加有关600个基因和蛋白质的信息 对于每个物种，口服元基因组的60,000多个新基因序列。这些系统发育 各种序列将促进重叠群的归因于其他元基因组的特定属或物种 项目。目前，基于16S rRNA序列，65％的口服原核生物仅被称为系统型。 有意义的生物学特征需要使生物体在长凳上操纵。目标3 将识别和沉积约200个未命名的口服系统型的参考菌株。菌株来自 表型表征的研究者培养物收集将通过16S rRNA序列鉴定 分析和新颖的参考菌株沉积了美国型文化收藏。该提议将 显着增强我们对人类微生物组的理解，并最终理解其 与口腔健康和疾病中宿主的互动。该建议是对PA-04-131的回应 口服微生物组的宏基因组分析。 这项研究将帮助我们了解人类口腔中生活的几百种细菌， 他们的基因。这些细菌会引起蛀牙，牙周疾病和其他地方的感染 身体。了解这些细菌的更多信息将使科学家能够开发出更好的治疗方法 并防止口腔疾病。