Investigation of commensal bacteria in controlling Pseudomonas aeruginosa airway infection

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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.