Metatramscriptome of the Oral Microbiome During Periodontal Disease Progression

牙周病进展过程中口腔微生物组的宏转录组

• 批准号: 8309806
• 负责人: Jorge Frias-Lopez
• 金额: $ 39.73万
• 依托单位: ADA FORSYTH INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-03 至 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8309806
• 关键词: Adult; Affect; American; Bioinformatics; Biometry; Cardiovascular Diseases; Censuses; Chronic; Clinic; Clinical; Clinical Research; Cloning; Communities; Compassion; Complementary DNA; Complex; Conduct Clinical Trials; DNA; Data Set; Databases; Development; Diabetes Mellitus; Diagnosis; Diagnostic; Disease; Disease Progression; Disorder by Site; Gene Expression; Gene Expression Profile; Genes; Genome; Goals; Health; In Situ; Individual; Inflammation; Institutes; Lesion; Lung diseases; Measures; Messenger RNA; Metabolic; Metagenomics; Methods; Microbial Biofilms; Molecular; Molecular Profiling; Monitor; Nucleotides; Oral; Organism; Outcome; Pathogenesis; Patients; Periodontal Diseases; Periodontal Infection; Periodontitis; Physiological; Polymerase Chain Reaction; Population; Prevalence; Prevention; Proteins; Public Health Schools; RNA; Relative (related person); Research; Research Personnel; Resources; Risk; Sampling; Site; Staging; Techniques; Tissues; Tooth Loss; Tooth structure; Translational Research; United States; Work; microbial; microbial community; microorganism; next generation; novel; oral biofilm; oral microbiome; prevent; programs; public health relevance; reproductive; subgingival biofilm

DESCRIPTION (provided by applicant): Periodontitis is a polymicrobial disease caused by the coordinated action of a complex microbial community, which results in inflammation of tissues that support the teeth. Periodontitis is a widespread and serious health condition that occurs in moderate form in 30% to 50% of American adults and in severe form in 10% of adults. The goal of this research program is to identify in situ the molecular mechanisms of pathogenesis by which periodontitis progress in some sites while in others the disease remains latent. Metagenomic and metatranscriptomic analysis (gene expression analysis of entire complex bacterial communities in situ) provides the information required to understand the activity and relative importance of the constituents in the pathogenic biofilm during periodontal infection. To this end we propose the following Specific Aims: Aim 1. Determine differences in prevalence and relative abundance of species in microbial communities from progressing and non-progressing periodontal sites. Aim 2. Identify in situ genes that are differentially expressed in microbial communities from progressing and non-progressing periodontal sites. We have successfully applied metatranscriptomic techniques to the study of environmental samples. The key step of the method to assess expression analysis in whole microbial communities is the linear amplification of small quantities of RNA extracted from the bacterial assemblages. The final amplified RNA is a direct representation of the relative abundance of mRNA in the original sample. The second aspect that facilitates metatranscriptomic analysis of whole bacterial communities is that pyrosequencing techniques allow now to sequence large amounts of DNA avoiding cloning biases associated with classical techniques. The target subject population will consist of 20 chronic periodontitis individuals. This subject population was chosen because chronic periodontitis is the most commonly encountered type of periodontitis and thus, the microbial changes observed will be relevant to a large proportion of subjects with periodontal disease. The patients will be followed monthly for a period of 6 months, during which they will undergo clinical monitoring to determine which samples will be used for compassion of progressing and non-progressing sites by metagenomic and metatranscriptomic analysis. Identification of critical genes that are required for pathogenesis and information about their differential expression can be used to develop novel targeted approaches to early-stage diagnosis, treatment, monitoring and prevention. Moreover, the potential impact extends beyond the study of periodontitis because the same principles and methods potentially can be applied to other polymicrobial diseases. We believe that the team we have assembled for this project (Forsyth Institute with help of Broad Institute and the Department of Biostatistics at Harvard School of Public Health) has all the qualifications to accomplish successfully the goals proposed in the present application. PUBLIC HEALTH RELEVANCE: Periodontitis is a polymicrobial disease caused by complex microbial community, which could result in the loss of teeth. The goal of this project is to understand which organisms are active and what they are doing during periodontitis progression to develop specific treatments against them.

描述（由申请人提供）：牙周炎是由复杂微生物群落的协调作用引起的多种疾病，这导致了支撑牙齿的组织的炎症。牙周炎是一种普遍且严重的健康状况，在30％至50％的美国成年人中以中等形式发生，而10％的成年人则以严重的形式发生。该研究计划的目的是原位确定发病机理的分子机制，在某些部位中，牙周炎在某些部位进展，而在另一些部位，这种疾病仍然潜在。宏基因组和元文字分析（对原位的整个复杂细菌群落的基因表达分析）提供了了解牙周感染期间致病生物膜中成分的活性和相对重要性所需的信息。为此，我们提出了以下特定目的：目标1。确定微生物群落中物种的患病率和相对丰度的差异，从进展和非培养牙周部位。 AIM 2。鉴定在微生物群落中差异表达的原位基因，从进展和非培养牙周位点。我们已成功地将元转录技术应用于环境样品的研究。评估整个微生物群落表达分析的方法的关键步骤是从细菌组合中提取的少量RNA的线性扩增。最终放大的RNA是原始样品中mRNA相对丰度的直接表示。促进整个细菌群落的元文字分析的第二个方面是，焦磷酸测序技术现在允许对大量的DNA进行大量避免与经典技术相关的克隆偏见。目标受试者将由20个慢性牙周炎个体组成。之所以选择该受试者，是因为慢性牙周炎是最常见的牙周炎类型，因此，观察到的微生物变化将与很大一部分患有牙周疾病的受试者有关。患者将每月遵循6个月的时间，在此期间，他们将接受临床监测，以确定哪些样品将通过元基因组和元文字分析来同情进展和非促进位点。鉴定发病机理所需的关键基因和有关其差异表达的信息可用于开发新颖的靶向方法，以进行早期诊断，治疗，监测和预防。此外，潜在的影响范围超出了牙周炎的研究，因为相同的原理和方法可能可以应用于其他多数型疾病。我们认为，我们为该项目组装的团队（在Broad Institute和Harvard Public Health学院的生物统计学系的帮助下，福赛斯研究所）拥有所有资格，可以成功实现本申请中提出的目标。 公共卫生相关性：牙周炎是由复杂的微生物群落引起的一种多性疾病，这可能导致牙齿丧失。该项目的目的是了解哪些生物是活跃的，以及它们在牙周炎进展过程中正在做的事情，以开发针对它们的特定治疗方法。