Oral microbial community structure and assembly: from molecule to microbiome

摘要 正如后生动物组织和器官的功能是由表型上的 口腔微生物在促进健康和疾病方面的功能来自不同的细胞， 它们的模式化结构的新特性：生物膜。例如，牙龈上的 牙菌斑在牙龈边缘形成稳定的、长距离的生物膜与可逆性牙龈炎有关， 可能发展为慢性牙周炎。最近的研究对两个因素的相对贡献提出了质疑。 长距离构建龈上菌斑的明显的丝状生物：梭杆菌属 具核棒状杆菌和马图霍氏棒状杆菌。有一个关键需要了解的作用， 丝状生物在生物膜组装中起作用，因为众所周知， 丰度、生态演替和生物膜结构介导了从健康到炎症的转变 口腔内的牙周病为了解决这一知识缺口，我们开发了一种体外口腔生物膜， 模型，适用于系统成像，研究远程社区结构的分子基础 和生物化学的相互作用。我们将阐明口腔生物膜组装中微米尺度空间结构的作用， 生长和功能，通过组合宏基因组测序和接种生物膜的系统成像， 健康捐赠者的牙菌斑我们将进一步定位新的棒状杆菌基因，涉及长 生物膜的范围空间结构，通过共培养RNA-seq和mRNA FISH成像。我们接下来将 破译特定的F.核质分子组分，其是长距离生物膜结构的基础， 靶向抑制F.核外膜蛋白与中和抗体，并通过遗传 这些蛋白质在大肠杆菌中的互补。大肠杆菌细胞与牙菌斑接种物共培养。知识 从本文的研究中获得的信息将包括对口头社区集会的整体理解 从分子到微生物组的空间尺度上的过程和物理结构， 干预牙菌斑介导的疾病进展的范例。

ABSTRACT Just as the function of metazoan tissues and organs is mediated by the patterned assembly of phenotypically distinct cells during development, the functions of oral microbes in promoting health and disease arise from the emergent properties of their patterned structure: the biofilm. For example, the accumulation of supragingival dental plaque into stable, long-range biofilms at the gingival margin is implicated in reversible gingivitis, which may progress to chronic periodontitis. Recent studies have called into question the relative contribution of two conspicuous, filamentous organisms in structuring supragingival plaque over long distances: Fusobacterium nucleatum and Corynebacterium matruchotii. There exists a critical need to understand the role that filamentous organisms play in biofilm assembly because it is well understood that changes in taxonomic abundance, ecological succession and biofilm structure mediate the transition from health to inflammatory periodontal diseases in the mouth. To address this knowledge gap, we have developed an in vitro oral biofilm model, amenable to systems imaging in which to study the molecular basis of long-range community structure and biochemical interaction. We will elucidate the role of micron-scale spatial structure in oral biofilm assembly, growth and function, through combined metagenomic sequencing and systems imaging of biofilms inoculated with dental plaque from healthy donors. We will further map novel Corynebacterium genes involved in long range spatial structure of biofilms, through co-culture RNA-seq and mRNA FISH imaging. We will next decipher the specific F. nucleatum molecular components that underly long-range biofilm structure, through targeted inhibition of F. nucleatum outer membrane proteins with neutralizing antibodies and through genetic complementation of these proteins in E. coli cells co-cultured with dental plaque inocula. The knowledge gained from the research proposed here will comprise a holistic understanding of oral community assembly processes and physical structure across spatial scales from molecule to microbiome and may identify new paradigms for intervening in the progression of dental plaque-mediated diseases.