Oral microbial community structure and assembly: from molecule to microbiome

摘要 就像后生动物组织和器官的功能是通过表型的图案化组装来调节的一样 在发育过程中，口腔微生物在促进健康和疾病方面的功能来自于 它们图案化结构的新特性：生物膜。例如，牙龈上积聚 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周炎有关， 可能进展为慢性牙周炎。最近的研究对两者的相对贡献提出了质疑 远距离形成牙周上菌斑的丝状菌：梭杆菌 核藻和马氏棒状杆菌。迫切需要了解这一角色 丝状菌在生物膜组装中发挥作用，因为众所周知，分类学上的变化 丰度、生态演替和生物膜结构介导了从健康到炎症的转变 口腔中的牙周病。为了解决这一知识缺口，我们开发了一种体外口腔生物膜。 适用于系统成像的模型，用于研究远程群落结构的分子基础 和生化相互作用。我们将阐明微米级空间结构在口腔生物膜组装中的作用， 通过联合元基因组测序和系统成像接种的生物膜的生长和功能 来自健康捐赠者的牙菌斑。我们将进一步定位与Long相关的新的棒状杆菌基因 通过共培养rna-seq和mRNAFISH成像研究生物膜的射程空间结构。接下来，我们将 通过以下途径破译构成长程生物膜结构的特定核藻分子成分 用中和抗体和遗传途径靶向抑制核盘藻外膜蛋白 这些蛋白质在与牙菌斑接种共培养的大肠杆菌细胞中的互补作用。《知识》 从这里提出的研究中获得的将包括对口腔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，并可能识别新的 干预牙菌斑介导性疾病进展的范例。

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.