Impact of Virome on Microbial Communities in the Respiratory Tract

总结/摘要 呼吸道病毒感染是肺功能进行性下降和发病的重要原因 慢性肺部疾病的患者，如囊性纤维化（CF）。呼吸道病毒感染 至少占成人CF患者肺部加重的50%，并与 肺功能、抗生素使用、住院时间延长和呼吸道症状增加。临床 研究还将病毒感染与慢性感染的发展联系起来，但潜在的 机制不明。在这项提案中，我们将测试新的假设，即病毒恶化改变了 CF中上呼吸道和/或下呼吸道的微生物组成，影响整体群落多样性 和功能，并损害肺功能。本研究具有创新性和探索性， 为未来的研究奠定基础，以揭示病毒-细菌相互作用的分子机制， 慢性肺病期间呼吸道的相互作用，也为评估 病毒急性发作对CF和其他慢性肺病疾病进展的影响。 在授予的R61阶段，我们将使用以前在一个过程中纵向收集的样本， 鼻内窥镜手术期间CF患者的鼻窦腔的年。在目标1中，我们将确定病毒是否 上呼吸道（URT）感染改变了URT的微生物群落。在目标2中，我们将 调查病毒感染塑造URT微生物组成的潜在机制，重点是 对偏斜的先天免疫反应和改变的营养免疫，以及采取公正的方法， 使用核糖体分析来评估病毒感染期间激活的功能途径， 城市轨道交通的微生物群落。 R33阶段将建立在R61阶段采用的初步数据和技术基础上， 病毒感染如何改变整个呼吸道的微生物组组成和功能， 改变预示肺功能。纵向、成对的鼻腔和痰液样本将在每隔 三个月换两年在目标3中，我们将研究病毒感染是否会改变微生物群落的结构。 URT或LRT，以及评估先天免疫或营养免疫的变化（即元素金属分析） 或微生物途径被激活，预测病毒感染期间肺功能下降。这一阶段将 在目标4中达到高潮，在体外研究中对关键微生物相互作用或途径进行建模， 目的3，使用我们独特的多微生物感染模型， CF患者 通过阐明病毒感染影响呼吸道微生物群落的机制， 我们的长远目标是找出新的治疗目标。

SUMMARY/ABSTRACT Respiratory viral infections contribute significantly to the morbidity and progressive decline in lung function experienced by patients with chronic lung diseases, such as cystic fibrosis (CF). Respiratory viral infections account for at least 50% of pulmonary exacerbations of adult CF patients and are linked to worsening of pulmonary function, antibiotic use, prolonged hospitalizations and increased respiratory symptoms. Clinical studies have also linked viral infections with the development of chronic infections, yet the underlying mechanisms are unknown. In this proposal, we will test the novel hypothesis that viral exacerbations alter the microbial composition of the upper and/or lower respiratory tract in CF, affecting both overall community diversity and function and impairing pulmonary function. This study is innovative and exploratory in nature and intended to lay the foundation for future studies to both uncover the molecular mechanisms underlying viral-bacterial interactions in the respiratory tract during chronic lung disease and also inform larger clinical studies that assess the impact of viral exacerbations on disease progression in CF and other chronic lung diseases. In the R61 phase of the award, we will use samples previously collected longitudinally over the course of one year from the sinonasal cavity of CF patients during endoscopic surgery. In Aim 1, we will determine if viral infections of the upper respiratory tract (URT) alter the microbial communities of the URT. In Aim 2, we will investigate potential mechanisms by which viral infections shape the microbial composition of the URT, focusing on skewed innate immune responses and altered nutritional immunity, as well as take an unbiased approach using ribosome profiling to assess functional pathways activated during viral infection that might shift the microbial communities of the URT. The R33 phase will build upon preliminary data and techniques adapted during the R61 phase to assess how viral infections alter the microbiome composition and function throughout the respiratory tract and if these alterations predict pulmonary function. Longitudinal, paired sinonasal and sputum samples will be collected every three months for two years. In Aim 3, we will examine if viral infections shift the microbial communities of the URT or LRT, as well as assess changes in innate immunity or nutritional immunity (i.e. elemental metals analysis) or microbial pathways activated that predict pulmonary function decline during viral infection. This phase will culminate in Aim 4 with mechanistic in vitro studies modeling key microbial interactions or pathways revealed in Aim 3, using our unique polymicrobial infection models with primary sinonasal and bronchial epithelial cells from CF patients. By elucidating mechanisms by which viral infections impact microbial communities in the respiratory tract, our long-term goal is to identify new therapeutic targets for intervention.