Spatial Organization of the Oral Microbiome

描述(申请人提供)：人类口腔被一个极其复杂的微生物群落定居，该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，可能必须以精细的分辨率探索独特微生态位中微生物群落的空间组织，以便为阐明群落聚集和功能的规则以及了解它们在疾病中的作用提供基础。虽然下一代DNA测序技术和元基因组学彻底改变了微生物群落的分析，但我们理解中的一个主要差距是缺乏微米级别的空间信息，这些信息是更好地表征微生物群落成员和宿主组织之间相互关系所必需的信息。我们建议通过海洋生物实验室的Borise实验室和Forsyth研究所的DeWhirst实验室和哈佛大学牙医学院的DeWhirst实验室之间的一项新合作来填补这一空白。博尔西实验室最近开发了一种组合标记和光谱成像(CLASI)策略，用于在一张显微图像中同时识别数十个微生物分类群。DeWhirst实验室对人类口腔微生物区系进行了开创性的微生物组研究。这两个实验室在ARRA挑战赠款的支持下进行了初步合作，将Clasi策略应用于人类牙菌斑的分析，这是一种微生物生物膜，并导致了一份以15种口腔分类群的接近关系为特征的“原则证明”出版物。在此基础上，我们提出的研究将可视化并定义9个口腔微生态位的微米级生物地理学：龈下菌斑、龈上菌斑、角化牙龈、硬腭部、舌背、颊粘膜、腭扁桃体、喉部和唾液。利用自动瓷砖扫描能力，它将记录牙周病中龈下微生物的结构，展示该方法用于检查其他口腔疾病的实用性。它将为口腔研究社区生产一套经过验证的鱼类探针。通过揭示口腔微生物组的精确、微米级结构，这项研究将解决群落动力学的基本机制和原则。它将为人类口腔微生物区系的成员是如何组织的提供了前所未有的系统水平的理解，并将为未来研究正常微生物群在健康和患病口腔中的作用奠定基础。它将通过开发方法、分析工具和探针来影响更广泛的口腔和微生物研究界。该项目应有助于确定可作为治疗干预的新靶点的关键细菌相互作用。

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 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 School of Dental Medicine. 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 microbiomic 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 relationshis of 15 oral taxa. Building on this foundation, our proposed research will visualize and define the micron-scale biogeography of the oral microbiome 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 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.