Spatial Organization of the Oral Microbiome

描述（由申请人提供）：人类口腔是一个极其复杂的微生物群落的定植，在人类健康和疾病中起着关键作用。人们越来越认识到，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测序技术和宏基因组学已经彻底改变了微生物群落的分析，但我们在理解上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成员（微生物相互作用组）与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Borisy实验室与Forsyth研究所和哈佛医学院的Dewhirst实验室之间的新颖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，用于在单个显微镜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群进行了突破性的宏基因组研究。在ARRA挑战基金的支持下，两个实验室之间进行了初步合作，将CLASI策略应用于人类牙菌斑（一种微生物生物膜）的分析，并发表了“原理证明”

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.