Investigation of commensal bacteria in controlling Pseudomonas aeruginosa airway infection

慢性铜绿假单胞菌感染有助于囊性纤维化（CF）患者的死亡率。最近一些来自气道微生物组测序的CF研究表明，共生菌可能是抑制铜绿假单胞菌感染相关疾病进展的重要因素之一。我们对从CF患者气道样本中分离的147株共生菌进行了筛选研究，以确定能够抑制铜绿假单胞菌的肺共生菌。10株（3种）在多次实验中均表现出强烈抑制铜绿假单胞菌生长和免疫刺激的一致结果。为了了解抑制机制和对宿主反应的潜在影响，我们将在精确切割的肺切片中进行共感染作为模型类器官系统。我们将通过双RNA-seq和单细胞RNA-seq检测铜绿假单胞菌/共生相互作用引发的铜绿假单胞菌和小鼠宿主的转录组变化。双重rna测序是必要的，因为干扰宿主反应以及中间细菌可能发生。使用精确切割的肺切片作为模型类器官系统，单细胞测序将揭示转录组变化的细胞分辨率。该应用程序建立在由“Mukoviszidose研究所”资助的一个正在运行的项目上，仅适用于额外的测序费用。本申请涉及三个重要的研究课题：1。鉴定铜绿假单胞菌/共生菌相互作用引发的铜绿假单胞菌转录组变化，了解特定共生菌株对铜绿假单胞菌的影响，并并行分析与铜绿假单胞菌相互作用是否也引发共生菌的转录组变化。2. 通过比较宿主对单铜绿假单胞菌感染和共感染的反应，研究铜绿假单胞菌/共感染对宿主防御的影响。3. 通过单细胞测序获取肺中不同细胞类型对单感染和共感染的反应信息。除了解决这些有针对性的问题外，该研究还将以探索性的方式用于产生指导进一步研究CF肺病中共生菌-病原体-宿主相互作用的见解。

Chronic Pseudomonas aeruginosa infections contribute to mortality in patients suffering from cystic fibrosis (CF). A few recent CF studies originating from airway microbiome sequencing suggest that commensal bacteria might be one of the important factors inhibiting disease progression related to P. aeruginosa infection. We have performed a screening study with 147 commensal bacterial strains isolated from airway samples of CF patients to identify lung commensal bacteria which are able to inhibit P. aeruginosa. 10 strains (3 species) showed consistent results in multiple experiments strongly inhibiting growth and immunostimulation of P. aeruginosa. To understand the mechanism of inhibition and the potential impact on host responses, we will do co-infections in precision cut lung slices as model organoid system. We will examine P. aeruginosa/commensal interaction-triggered transcriptomic changes in P. aeruginosa and in mouse host by dual RNA-seq as well as single-cell RNA-seq. Dual RNA-seq is necessary as interferences with host responses as well as in-between bacteria can occur. Using precision cut lung slices as model organoid system, single-cell sequencing will reveal cellular resolution of the transcriptome changes. The application builds on a running project funded by the “Mukoviszidose Institut” and only applies for additional sequencing costs. This application addresses three important research topics: 1. Identification of P. aeruginosa/commensal interaction-triggered transcriptomic changes in P. aeruginosa to understand how P. aeruginosa is affected by certain commensal strain, and in parallel analyzing if there are also transcriptomic changes in commensal bacteria triggered by the interaction with P. aeruginosa. 2. Examination of the impacts of co-infection by P. aeruginosa/commensal on host defenses by comparing host-responses to P. aeruginosa mono-infection and to co-infection. 3. Acquisition of information about how different cell types in the lung react to mono-infection and co-infection by single-cell sequencing. In addition to addressing these targeted questions, the study will also be used in an exploratory manner to generate insights directing the further investigation of the commensal-pathogen-host interactions in the CF lung disease.