Ecology of Cystic Fibrosis

描述（由申请人提供）：囊性纤维化（CF）是一种显著降低预期寿命和质量的遗传性疾病。该病的特点是多微生物感染，导致肺部重塑和气道粘液堵塞。CF患者经历间歇性恶化，导致气道瘢痕形成，最终导致呼吸严重受损。尽管积极治疗，大多数CF患者将死于慢性肺部感染引起的呼吸衰竭。标准的临床微生物学研究和抗生素敏感性测试在预测特定治疗的医疗结果方面存在严重局限性。这部分是由于在CF肺中微生物及其病毒捕食者（噬菌体）的动力学基本上是未知的。本研究的目的是使用宏基因组学和显微镜来表征这两个群落，并确定它们如何响应诸如疾病严重程度、抗生素治疗和旨在破坏粘液塞的化学治疗等扰动而变化。宏基因组数据将用于确定病毒和微生物群落的类型和代谢功能如何变化。微生物生长速率和噬菌体介导的死亡也将被测量。为了更好地了解微生物和病毒群落的空间动态，我们还将解剖CF患者的肺部。将对来自各个叶的病毒和微生物宏基因组进行测序。为了确定特定种类的微生物在粘液塞中的位置，将对组织样品使用16S rDNA探针进行荧光原位杂交。这些数据集将用于参数化CF肺的三个互补生态模型。然后，这些模型将用于替代治疗方案的计算机测试（例如，调整抗生素给药的时间）。完成后，我们将对CF中的病毒和微生物群落以及它们对治疗的反应产生前所未有的看法。有了这些模型，我们将能够更好地了解这些社区的动态，并测试替代治疗方案，以延长和改善CF患者的生命。

DESCRIPTION (provided by applicant): Cystic Fibrosis (CF) is a genetic disease that dramatically decreases life expectancy and quality. The disease is characterized by polymicrobial infections, which lead to lung remodeling and airway mucus plugging. CF patients experience intermittent exacerbations that cause airway scarring and eventually result in seriously impaired respiration. Despite aggressive therapy, most CF patients will die from respiratory failure caused by the chronic lung infections. Standard clinical microbiological studies and antibiotic susceptibility testing have severe limitations in predicting medical outcomes from specific therapies. This is due in part because the dynamics of microbes and their viral predators (phage) are essentially unknown in the CF lung. The goal of this study is to use metagenomics and microscopy to characterize these two communities and determine how they change in response to perturbations such as disease severity, antibiotic treatments, and chemical treatments designed to break up the mucus plugs. The metagenomic data will be used to determine how the types and metabolic functions of both the viral and microbial communities change. Microbial growth rates and phage-mediated death will also be measured. To better understand the spatial dynamics of the microbial and viral communities, we will also be dissecting lungs of CF patients. Viral and microbial metagenomes from individual lobes will be sequenced. To determine where specific species of microbes reside in the mucus plugs, fluorescent in situ hybridization with 16S rDNA probes will used on tissue samples. Together these data sets will be used to parameterize three complementary ecological models of the CF lung. Then these models will be used as in silico tests of alternative treatment regimes (e.g., adjust timing of antibiotic administration). When completed, we will have generated an unprecedented view of the viral and microbial communities in CF and how they respond to treatments. With the models, we will be able to better understand the dynamics of these communities and test alternative treatment regimes to prolong and improve the lives of CF patients. PUBLIC HEALTH RELEVANCE: It is increasingly recognized that ecological approaches can help control infectious diseases and promote human health. The goal of this proposal is to use microbial ecology methods to better understand and control the devastating disease Cystic Fibrosis.