Cultivation, Nature, Ecology and Pathogenicity of the Uncultivable Oral Microbiom

不可培养口腔微生物的培养、性质、生态和致病性

• 批准号: 8885797
• 负责人: Eric John Alm
• 金额: $ 146.54万
• 依托单位: ADA FORSYTH INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-03 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8885797
• 关键词: Accounting; Address; Air; Animal Model; Bacteria; Biochemical Pathway; Bioinformatics; Bypass; Cell Communication; Cells; Clinical; Coculture Techniques; Communities; Conditioned Culture Media; Culture Media; Data; Databases; Dental caries; Dependence; Dependency; Development; Devices; Disease; Disease Progression; Dorsal; Drug Formulations; Ecology; Environment; Environmental Microbiology; Evolution; Fractionation; Future; Genome; Genomics; Goals; Growth; Growth Factor; Health; Healthcare; Helper-Inducer T-Lymphocyte; Human; Human Microbiome; Image; Imaging technology; Immune response; In Vitro; Incubated; Infection; Inflammation; Inflammatory Response; Informatics; Integration Host Factors; Knowledge; Metabolic; Methods; Microbiology; Microfluidics; Modeling; Mouth Diseases; Mutation; Nature; Nutrient; Nutritional; Nutritional Requirements; Oral; Oral cavity; Oral health; Oryctolagus cuniculus; Pathogenicity; Periodontal Diseases; Play; Population; Prevalence; Prevention; Production; Recording of previous events; Research; Research Personnel; Role; Sampling; Science; Signal Transduction; Site; Surface; System; Taxon; Technology; Testing; Therapeutic Intervention; Vaccines; auxotrophy; base; improved; in vivo; innate immune function; innovation; innovative technologies; macrophage; member; metabolomics; microbial; microbiome; monocyte; multidisciplinary; neutrophil; novel; oral bacteria; oral microbiome; pathogen; pathogenic bacteria; prevent; response; spectrograph; web-accessible

DESCRIPTION (provided by applicant): A full understanding of human oral health and disease requires a comprehensive analysis of the human oral microbiome and its interactions with the human host. A significant barrier to this goal is that 35% of the predominant human microbiota are uncultivable using standard cultivation methods. This proposal addresses the goals of RFA-DE-14-003: Innovative Approaches and Technologies for Examining the Uncultivated Bacteria of the Oral Microbiota through a multidisciplinary, team science approach, bringing together experts in microbiology, genomics, metabolomics, informatics, microfluidics and imaging. The specific aims have been constructed to achieve a systems-level integration of state-of-the-art technologies and innovative approaches. The proposal is hypothesis driven; it will provide specific knowledge on the nature of uncultivability for all uncultivated oral taxa identified in a subject population. This proposal will likely establish a new paradigm for cultivating previously uncultivable members of the oral microbiota by culturing first in consortia, rapidly reducing the complexity of the consortia, and bringing them into co-cultivation as binary pairs in commensal or syntrophic relationships. Clinical samples containing uncultivated bacteria will be incubated under novel growth conditions to enrich for reduced consortia containing uncultivables and helper species that supply essential nutrients. We will use bioinformatic and metabolic modeling approaches to determine the importance of auxotrophy and to identify novel growth factors. The proposal is the first to track genome evolution in studies to determine the genetic changes underlying bacterial domestication. Compounds that support the growth of previously uncultivable taxa will be identified and allow the formulation of novel culture media to support routine cultivation of a broader range of the oral microbiota. The identity of unknown nutrients will be determined by mass spectrometric methods. We will use novel micro-fluidic devices and spectral imaging technology to examine bacteria-bacteria and bacteria-host cell interactions of previously-uncultivable bacteria with other cells. Microfluidic systems will be used to quantify growth of uncultivable species in reduced consortia, in binary pairs, or when supplemented with a required metabolite or host factor. Periodontal disease studies using mock communities will provide an under-standing of the impact of previously-uncultivable bacteria on the commensal microbiota, the progression of disease, the host immune and inflammatory responses to pathogenic consortia, and the response of neutrophils and monocytes to previously-uncultivable bacteria alone or in pathogenic consortia. A web-accessible database on the prevalence, cultivation status, co-cultivation partners, auxotrophies, and domestication histories of previously-uncultivated taxa will be created for ready access to the scientific community. Isolates will be available for in vivo and in vitro studies of ecological interactions and interactions with the host. The high-throughput methods developed to cultivate currently- uncultivable oral bacteria will be generalizable to other body sites and to environmental microbiology.

描述（由申请人提供）：对人类口腔健康和疾病的充分理解需要对人口腔微生物组及其与人类宿主的相互作用进行全面分析。这一目标的一个重要障碍是，使用标准培养方法，35％的人类微生物群是无法培养的。该提案解决了RFA-DE-14-003的目标：通过多学科，团队科学方法研究口腔微生物群的未养殖细菌的创新方法和技术，将微生物学，基因组学，代谢组学，信息素学，微生物学，微生物学和成像的专家聚集在一起。已经构建了具体目标，以实现最先进的技术和创新方法的系统级集成。该提议是由假设驱动的。它将为所有在受试者人群中确定的所有未经耕种的口服分类单元的不可养生性的性质提供具体知识。该提案可能会建立一个新的范式，用于通过首先在财团中培养口头微生物群以前无法培养的成员， 迅速降低了财团的复杂性，并将它们作为共生或综合关系中的二进制对进行共培养。在新的生长条件下将孵育含有未养殖细菌的临床样品，以富集含有不可培养物和提供必需营养物质的辅助物质的财团。我们将使用生物信息学和代谢建模方法来确定合并营养的重要性并确定新颖的生长因子。该提案是第一个在研究中跟踪基因组进化的提案，以确定细菌驯化的遗传变化。将确定支持先前无法培养的分类单元增长的化合物，并允许新型培养基的制定支持更广泛的口服微生物群的常规培养。未知营养素的身份将通过质谱法确定。我们将使用新型的微富集设备和光谱成像技术来检查以前可培养细菌与其他细胞的细菌 - 细菌和细菌宿主宿主相互作用。微流体系统将用于量化不可养殖物质在减少的财团，二进制对或补充所需的代谢物或宿主因子时的生长。使用模拟群落的牙周疾病研究将为以前可培养的细菌对共生微生物群，疾病的进展，对病原体的宿主免疫和炎症反应以及中性粒细胞和单核细胞对以前可培养的细菌的反应的影响提供不明显的影响。将创建有关以前分类的分类单元的流行，培养状况，共培养伙伴，相互作用的伙伴，合作伙伴和驯养历史的可访问数据库的可及其。分离株将用于体内和体外研究生态学 与主机的互动和互动。开发的用于培养目前不可培养的口服细菌的高通量方法将推广到其他身体部位和环境微生物学。