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: 8737392
• 负责人: Eric John Alm
• 金额: $ 150.89万
• 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/8737392
• 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; public health relevance; response; 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）：要全面了解人类口腔健康和疾病，需要对人类口腔微生物组及其与人类宿主的相互作用进行全面分析。实现这一目标的一个重大障碍是 35% 的主要人类微生物群无法使用标准培养方法进行培养。该提案解决了 RFA-DE-14-003 的目标：通过多学科、团队科学方法检查口腔微生物群中未培养细菌的创新方法和技术，汇集了微生物学、基因组学、代谢组学、信息学、微流体学和成像领域的专家。具体目标是实现最先进技术和创新方法的系统级集成。该提案是假设驱动的；它将提供关于在主题群体中确定的所有未培养的口腔类群的不可培养性质的具体知识。该提案可能会建立一个新的范例，通过首先在联合体中培养来培养以前无法培养的口腔微生物群成员， 迅速降低联盟的复杂性，并将它们作为共生或互养关系中的二元对进行共同培养。含有未培养细菌的临床样本将在新的生长条件下进行培养，以丰富含有不可培养细菌和提供必需营养的辅助物种的减少菌群。我们将使用生物信息学和代谢建模方法来确定营养缺陷型的重要性并识别新的生长因子。该提案是第一个在研究中追踪基因组进化以确定细菌驯化背后的遗传变化的提案。支持以前无法培养的类群生长的化合物将被鉴定出来，并允许配制新型培养基来支持更广泛的口腔微生物群的常规培养。未知营养素的身份将通过质谱方法确定。我们将使用新型微流体装置和光谱成像技术来检查以前无法培养的细菌与其他细胞之间的细菌-细菌和细菌-宿主细胞相互作用。微流体系统将用于量化减少的聚生体、二元对中或补充所需代谢物或宿主因子时不可培养物种的生长。使用模拟群落进行的牙周病研究将有助于了解以前无法培养的细菌对共生微生物群的影响、疾病的进展、宿主对致病菌群的免疫和炎症反应，以及中性粒细胞和单核细胞对以前无法培养的细菌的反应。无法单独培养的细菌或致病菌群。将创建一个可通过网络访问的数据库，内容涉及先前未栽培的类群的流行率、栽培状况、共培养伙伴、营养缺陷型和驯化历史，以便科学界随时访问。分离物将可用于生态学的体内和体外研究 互动以及与主人的互动。为培养目前无法培养的口腔细菌而开发的高通量方法将推广到其他身体部位和环境微生物学。