Spatial characterization of microbial communities in the cystic fibrosis lung

描述（由申请人提供）：人类微生物组因其与宿主健康和疾病的联系而受到广泛关注。囊性纤维化尤其如此 呼吸道，其中复杂的微生物群落被认为是患者死亡的主要原因。除了铜绿假单胞菌，最近非培养研究的激增产生了越来越多的可疑病原体及其与疾病进展的相关性。然而，我们无法有效地治疗这些患者仍然是由于缺乏对CF肺环境的了解以及特定化学参数如何定义给定细菌物种的存在或不存在。在自然环境中，如海洋沉积物中，确定环境化学对微生物群落的影响对于充分了解给定的生态系统至关重要。然而，这种方法在医学微生物学背景下很少使用。在这里，我的首要目标是应用标准的环境微生物学原理和方法来测试支气管树的复杂化学在多个尺度上影响其常驻微生物区系的假设。最近，我们发现一类微生物产生的代谢物（吩嗪），微生物组组成和肺功能下降之间存在高度显著的相关性。在该奖项的K99阶段，总体目标将是扩大这些初步观察，并广泛研究囊性纤维化肺环境对其微生物组的影响。使用一组 在儿科患者中，我将首先测试吩嗪改变铁的氧化还原状态，这最终与整体肺部微生物组和疾病进展的变化相关。此外，我将使用新的成像方法来研究单个物种（特别是铜绿假单胞菌）在单细胞水平上对环境化学变化的细胞反应（特别是对铁的反应）。这些研究将揭示使用单细胞转录活性作为气道周围环境的直接读出的潜力，并且将潜在地指导基于环境化学的新型疗法的设计。接下来，我们将把这些方法应用于肺标本，以更好地了解整个支气管树微生物群落的空间异质性。有了这些信息，这些研究最终将在R00阶段扩大，以包括呼吸道内的其他代谢物和化学参数，以及宿主内的其他感染部位。 总而言之，这种理解微生物感染生态学的系统方法将改变我们对微生物组及其与健康和疾病联系的看法，并有可能开发新的治疗策略。

DESCRIPTION (provided by applicant): The human microbiome is gaining widespread attention for its link to host health and disease. This is particularly true of the cystic fibrosis airways, where a complex microbial community is recognized to be the major cause of patient mortality. In addition to Pseudomonas aeruginosa, a recent surge in culture- independent studies has generated a growing list of suspected pathogens and their correlation to disease progression. Yet, our inability to effectively treat these patients remains due to a lack of understanding of the CF lung environment and how specific chemical parameters define the presence or absence of a given bacterial species. In natural environments, such as a marine sediment, defining the effect of environmental chemistry on the microbial community is paramount in fully understanding a given ecosystem. Yet, this approach in a medical microbiology context is seldom used. Here, my overarching goal is to apply standard environmental microbiology principles and methodologies to test the hypothesis that the complex chemistry of the bronchial tree affects its resident microflora on multiple scales. Recently, we discovered a highly significant correlation between a class of microbially-produced metabolites (phenazines), microbiome composition, and lung function decline. In the K99 phase of this award, the overall goal will be to expand on these initial observations, and to broadly investigate the effect of the cystic fibrosis lung environment on its microbiome. Using a cohort of pediatric patients, I will first test that phenazines alter the redox state of iron, which ultimatey correlates to a shift in the overall lung microbiome and disease progression. In addition, I will use novel imaging methods to investigate the cellular response of individual species (particularly P. aeruginosa) at the single cell level to changes in environmental chemistry (specifically in response to iron). These studies will reveal the potential of using single cell transcriptional activity as a direct readout of the ambient environment of the airways, and will potentially guide the design of novel therapeutics based on environmental chemistry. Next, we will apply these methods to explanted lung samples in order to better understand the spatial heterogeneity of microbial communities throughout the bronchial tree. With this information in hand, these studies will ultimately be expanded in the R00 phase of the award to include other metabolites and chemical parameters within the respiratory tract, and other sites of infection within the host. Altogether, this systems approach to understanding the ecology of microbial infections will change the way we think about the microbiome and its link to health and disease, and has the potential for development of novel therapeutic strategies.