Spatial Organization of the Oral Microbiome

描述（由申请人提供）：人类口腔中定植着一个极其复杂的微生物群落，在人类健康和疾病中起着关键作用。越来越多的人认识到，在独特的微生态位的微生物群落的空间组织可能必须在精细的分辨率进行探索，以提供阐明社区组装和功能的规则，并了解它们在疾病中的作用的基础。虽然下一代DNA测序技术和宏基因组学已经彻底改变了微生物群落的分析，但我们理解的一个主要差距是缺乏微米级的空间信息，这些信息是更好地表征微生物群落（微生物相互作用组）成员之间的相互关系以及与宿主组织之间的相互关系所必需的。我们建议通过海洋生物实验室的Borisy实验室与福赛斯研究所和哈佛医学院的Dewhirst实验室之间的新型合作来填补这一空白。Borisy实验室最近开发了一种组合标记和光谱成像（CLASI）策略，用于在单个显微图像中同时识别数十种微生物分类群。Dewhirst实验室对人类口腔微生物进行了开创性的宏基因组研究。在ARRA挑战基金的支持下，两个实验室之间的初步合作将CLASI策略应用于人类牙菌斑（一种微生物生物膜）的分析，并导致了一份“原理证明”出版物，该出版物描述了这种接近性。 15个口腔分类群的关系。在此基础上，我们提出的研究将可视化和定义9个口腔小生境的口腔微生物组结构和相互作用组的微米级微生物学：龈下菌斑，龈上菌斑，角化牙龈，硬腭，舌背，颊粘膜，腭扁桃体，喉咙和唾液。采用自动瓷砖扫描能力，它将记录牙周病龈下微生物的结构和相互作用组，展示该方法用于检查其他口腔疾病的实用性。它将为口腔研究界提供一套经过验证的FISH探针。通过揭示口腔微生物组的精确的微米级结构，这项研究将解决社区动态的基本机制和原则。它将为人类口腔微生物群成员的组织方式提供前所未有的系统水平的理解，并将为未来研究健康和患病口腔中正常微生物植物群的作用奠定基础。它将通过开发方法，分析工具和探针影响更广泛的口腔和微生物研究社区。该项目将导致确定关键的细菌相互作用，可能作为治疗干预的新靶点。

DESCRIPTION (provided by applicant): The human mouth is colonized by a microbial community of enormous complexity that plays a key role in human health and disease. Increasingly, it is recognized that the spatial organization of microbial communities in unique micro-niches may have to be explored at fine resolution to provide the basis for elucidating the rules of community assembly and function and to understand their role in disease. Although next-generation DNA sequencing technology and metagenomics have revolutionized the analysis of microbial communities, a major gap in our understanding is the lack of spatial information at the micron level,--information necessary to better characterize the interrelationships between members of a microbial community (the microbial interactome) and with host tissue. We propose to fill this gap through a novel collaboration between the Borisy lab at the Marine Biological Laboratory and the Dewhirst lab at the Forsyth Institute and Harvard Medical School. The Borisy lab has recently developed a Combinatorial Labeling and Spectral Imaging (CLASI) strategy for the simultaneous identification of tens of microbial taxa in a single microscopic image. The Dewhirst lab has carried out ground-breaking metagenomic studies of the human oral microbiota. An initial collaboration between the two laboratories, supported by an ARRA Challenge Grant, applied the CLASI strategy to the analysis of human dental plaque, a microbial biofilm, and led to a "proof-of-principle" publication that characterized the proximity relationships of 15 oral taxa. Building on this foundation, our proposed research will visualize and define the micron-scale biogeography of the oral microbiome structure and interactome for 9 oral niches: subgingival plaque, supragingival plaque, keratinized gingivae, hard palate, tongue dorsum, buccal mucosa, palatine tonsils, throat, and saliva. Employing an automated tile-scanning capability, it will document the architecture and interactome for subgingival microbes in periodontal disease, demonstrating the utility of the approach for examining other oral diseases. It will produce a validated set of FISH probes for the oral research community. By revealing the precise, micron-scale structure of the oral microbiome, this research will address fundamental mechanisms and principles of community dynamics. It will provide an unprecedented systems-level understanding for how members of the human oral microbiota are organized and it will lay the foundation for future studies examining the role of the normal microbial flora in both healthy and diseased mouths. It will impact the broader oral and microbial research communities by developing methods, analysis tools and probes. This project should lead to the identification of key bacterial interactions that may serve as novel targets for therapeutic intervention.