Functional Genomics of Single- and Mixed-Species Biofilms in Spatiotemporal Scale

描述(申请人提供)：口腔、生殖器、呼吸道和肠道微生物群的细菌可以作为宿主相关的生物膜群落存在，与生物膜相关的感染是临床医生治疗的最严重的疾病之一。在全球范围内，对生物膜结构微环境内的细菌联合和动态了解甚少。在时间尺度上研究整个生物膜的全球基因表达动力学，缺乏对生物膜微环境中细菌生理和相互作用的分辨率。因此，全球基因表达动态在空间和时间两个维度上不同，这调节了细菌在其生物膜微环境中的生理。我们在单细胞转录组分析方面取得的最新进展使在细菌的微环境中进行精细分辨率的功能基因组分析成为可能。我们对铜绿假单胞菌(PA)单物种生物膜的初步数据在其生物膜微环境及其有组织的空间基因表达模式中产生了许多有趣的方面，这些空间基因表达模式构成了活的和功能的生物膜作为一个整体。在此，我们进一步提出了PA和Burkholderia cenocepacia(BC)的单一物种和混合物种生物膜模型，以开始解开时空全球基因表达模式的过程，该模式有助于细菌在其生物膜微环境中的生理和相互作用。Aim 1将确定PA和Bc在成熟的单一物种生物膜中的全球基因表达动力学和生理学，Aim 2将在体外确定PA和Bc在混合生物膜中的全球基因表达动力学、生理学和相互作用，并在体内进行验证。在完成这些研究后，我们希望在全球范围内发现关于细菌生理动态、单物种生物膜和混合生物膜微环境中的相互作用和合作的许多神秘问题的答案。这将作为进一步研究其他宿主相关生物膜群落和许多重要的生物膜相关感染的功能基因组学的基础和框架，从而产生新的治疗策略。

DESCRIPTION (provided by applicant): Bacteria of the oral, genital, respiratory, and gut microbiomes can exist as host- associated biofilm communities and biofilm-related infections are among the most serious diseases treated by clinicians. Bacterial associations and dynamics within the microenvironments of the biofilm structure are poorly understood on a global level. Global gene-expression dynamics of whole biofilms have been studied on the temporal scale, which lacks the resolution to decipher bacterial physiology and interactions within the microenvironments of biofilm. Thus, global gene-expression dynamics vary in two dimensions, space and time, which modulate the physiology of bacteria within their biofilm microenvironments. We have made recent advances in transcriptome analysis of single-cells have made fine-resolution functional genomic analysis of bacteria within their microenvironments possible. Our preliminary data of Pseudomonas aeruginosa (Pa) single-species biofilm has yielded many interesting aspects of this bacterium in its biofilm microenvironments and its organized spatial gene-expression pattern that make- up the living and functioning biofilm as a whole. Herein, we further proposed single- and mixed-species biofilm models of Pa and Burkholderia cenocepacia (Bc) to begin the process of unraveling the spatiotemporal global gene-expression pattern that contributes to the physiological- and interactions-dynamics of bacteria within their biofilm microenvironments. Aim 1 will determine the global gene-expression dynamics and physiology of Pa and Bc within mature single-species biofilms and Aim 2 will determine the global gene-expression dynamics, physiology, and interactions of Pa and Bc within mixed-species biofilms spatiotemporally in vitro, with validation in vivo. Upon completion of these studies, we expect to discover numerous answers to mysterious questions regarding the dynamics of bacterial physiology, interaction, and cooperation within microenvironments of single- and mixed-species biofilms at a global level. This will serve as a foundation and framework to further study the functional genomics of other host- associated biofilm communities and many important biofilm-related infections leading to novel treatment strategies.