Spatial characterization of microbial communities in the cystic fibrosis lung

项目摘要 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。这是 尤其是囊性纤维化气道，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，最近培养的激增- 独立研究已经产生了越来越多的可疑病原体及其与疾病的相关性 进展然而，我们无法有效地治疗这些患者仍然是由于缺乏对 CF肺环境以及特定的化学参数如何定义给定的 细菌种类在自然环境中，如海洋沉积物，确定环境影响 对微生物群落的化学研究对于充分了解特定的生态系统至关重要。但这 很少使用医学微生物学背景下的方法。在这里，我的首要目标是应用标准 环境微生物学原理和方法来测试假设，复杂的化学 支气管树在多个尺度上影响其驻留的微生物区系。 最近，我们发现了一类微生物产生的代谢产物 （吩嗪），微生物组组成和肺功能下降。在本奖项的K99阶段， 我们的目标将是扩大这些初步观察，并广泛调查囊性纤维化的影响， 肺部环境对其微生物组的影响使用一组儿科患者，我将首先测试吩嗪改变 铁的氧化还原状态，最终与整个肺部微生物组和疾病的变化相关 进展此外，我将使用新的成像方法来研究个体的细胞反应， 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影响（特别是 铁）。这些研究将揭示使用单细胞转录活性作为直接的生物学方法的潜力。 呼吸道周围环境的读出，并将潜在地指导新疗法的设计 基于环境化学。接下来，我们将把这些方法应用于分离的肺样本， 更好地了解整个支气管树微生物群落的空间异质性。与此 这些研究最终将在R 00阶段扩大，以包括其他 呼吸道内的代谢物和化学参数以及宿主内的其他感染部位。 总之，这种理解微生物感染生态学的系统方法将改变我们 思考微生物组及其与健康和疾病的联系，并有潜力开发新的 治疗策略

Project Summary 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 ultimately 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.