Spatial characterization of microbial communities in the cystic fibrosis lung

项目摘要 人类微生物群因其与宿主健康和疾病的联系而受到广泛关注。这是 尤其是囊性纤维化呼吸道，在那里复杂的微生物群落被认为是 病人死亡的主要原因。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 进步。然而，我们无法有效地治疗这些患者仍然是因为缺乏对 Cf肺环境和特定化学参数如何定义给定的 细菌种类。在自然环境中，如海洋沉积物中，定义环境的影响 微生物群落的化学对于充分理解一个特定的生态系统是至关重要的。然而，这 在医学微生物学的背景下，方法很少使用。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，以检验复杂化学的假设 支气管树在多个尺度上影响其驻留的微生物区系。 最近，我们发现一类微生物产生的代谢物之间存在高度显著的相关性。 (吩嗪类)、微生物组组成和肺功能下降。在这个奖项的K99阶段，总的 目标将是在这些初步观察的基础上进行扩展，并广泛调查囊性纤维化的影响。 肺环境对其微生物群的影响。使用一组儿科患者，我将首先测试吩嗪类药物改变 铁的氧化还原状态，最终与整个肺微生物群和疾病的转变相关 进步。此外，我将使用新的成像方法来研究个体的细胞反应 单细胞水平上的物种(特别是铜绿假单胞菌)对环境化学变化(特别是 对铁的反应)。这些研究将揭示利用单细胞转录活性作为直接 读出呼吸道的周围环境，并可能指导新疗法的设计 以环境化学为基础。接下来，我们将把这些方法应用于移植的肺样本，以便 更好地了解整个支气管树微生物群落的空间异质性。有了这个 信息，这些研究最终将在颁奖的R00阶段扩大到包括其他 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的系统方法将改变我们的方式 思考微生物群及其与健康和疾病的联系，并具有开发潜力的小说 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.