Determination of immunogenic microbiota in the lung: leveraging the Lung HIV Microbiome Project

项目摘要 慢性阻塞性肺疾病（COPD）包括气道阻塞和/或肺气肿， 在当今时代，这是艾滋病毒阳性个体发病率和死亡率不断上升的原因。艾滋病毒的发病机制- 相关的COPD知之甚少，但肺部微生物组的变化可能起作用。肺与 与宿主免疫系统接触，并持续暴露于环境和微生物 从口腔中吸出。我们还不知道这些暴露如何影响肺部，以及如何影响肺部。 在HIV和COPD中，肺部微生物可能不同。目前的研究将利用数据， 来自肺部HIV微生物组项目（LHMP）的生物标本，这是肺部微生物组的第一项多中心研究。 该项目将通过开展基于微生物组的（微生物群落， 基因含量和环境相互作用）检查肺，同时发展或 增强了高通量的基于组学的技术的使用。首先，我们将研究如何主机识别 在HIV感染者和未感染者之间，以及在有和没有感染者之间， 慢性阻塞性肺病使用LHMP支气管肺泡灌洗（BAL）标本，我们将确定驱动 使用新型磁激活细胞分选（MACS）测定靶向和分离宿主应答 免疫球蛋白（IG）结合细菌和真菌。然后，我们将使用测序技术比较分类学 感染和不感染HIV的个体之间以及感染和不感染COPD的个体之间Ig结合细菌的差异。选择 还将测量人宿主产生的趋化因子和细胞因子（小信号分子）， 提供宿主免疫系统状态的快照。然后，我们将描述的生物功能， 微生物组更广泛地使用整个社区RNA来测量不仅细菌， 真菌、古细菌和噬菌体也可能有贡献。一系列比较生物信息学和 统计方法将用于描述和比较群落结构和功能之间 有和没有HIV和COPD的人。这些方法的发展不仅揭示了 分类学结构与宿主免疫识别有关，但通过RNA测序，也能识别 生物功能。了解集体微生物群落的功能将使我们能够更好地解决 问题是如何代谢的社区居住在肺的个人与艾滋病毒和 COPD与没有这些条件的个体不同，他们的代谢活动在哪些方面起作用 肺功能的变化总的来说，这项研究将检查肺微生物群落在个人与 不同的HIV和COPD状态，形成了大规模机制研究的基础， 该方法直接适用于其他基于微生物组的肺部健康和疾病研究。

PROJECT SUMMARY Chronic obstructive pulmonary disease (COPD), which encompasses airway obstruction and/or emphysema, is a growing cause of morbidity and mortality in HIV+ individuals in the current era. Pathogenesis of HIV- associated COPD is poorly understood, but shifts in the lung microbiome may play a role. The lung interacts with the host immune system and receives constant exposure to the environment and to microorganisms aspirated from the oral cavity. We do not yet know how these exposures might impact the lung and how microorganisms in the lung might differ in HIV and in COPD. The current study will leverage data and biospecimens from the Lung HIV Microbiome Project (LHMP), the first multicenter study of the lung microbiota. This project will add to the LHMP framework by undertaking a microbiome-based (microbial communities, their gene content, and environmental interactions) examination of the lung while simultaneously developing or enhancing the use of high throughput ‘omics-based technologies. First, we will examine how host recognition of microorganisms differs between HIV-infected and uninfected individuals and individuals with and without COPD. Using LHMP bronchoalveolar lavage (BAL) specimens, we will identify key bacteria and fungi that drive host response using a novel magnetic activated cell sorting (MACS) assay to target and separate immunoglobulin (Ig)-bound bacteria and fungi. We will then use sequencing techniques to compare taxonomy of Ig-bound bacteria between individuals with and without HIV and with and without COPD. Selected chemokines and cytokines (small signaling molecules) produced by the human host will also be measured to provide a snapshot of host immune system status. We will then characterize the biological functions of the microbiome more broadly using whole community RNA to measure metabolic activity of not only bacteria, but also potential contributions from fungi, archaea and bacteriophage. A series of comparative bioinformatic and statistical approaches will be used to characterize and compare community structure and function between individuals with and without HIV and COPD. Development of these methods will reveal not only shifts in taxonomic structure in relation to host immune recognition, but through sequencing RNA, also identify biological function. Understanding collective microbial community function will allow us to better address the question of how does the metabolism of the community that resides in the lung of individuals with HIV and COPD differ from individuals without these conditions, and in what ways may their metabolic activity contribute to changes in lung function. Collectively, this study will examine lung microbial communities in individuals with differing HIV and COPD status, forming the foundation for larger-scale mechanistic studies while developing methodology directly applicable to other microbiome-based lung studies of health and disease.