The murine lung microbiome and its disbalance by the fungal lung pathogen Aspergillus fumigatus

The presence of a stable residential microbiota in the lungs and their potential function for health and disease remain a matter of debate. Moreover, little is known about interconnections between the lung microbiota and lung diseases e.g. caused by pathogenic microorganisms. Aspergillus fumigatus is a clinically relevant fungus causing life-threatening lung infections in immunocompromised patients. Here, we aimed to analyze the lung microbiota of mice both by DNA sequencing and cultivation approaches. This way, we aimed at the identification of the species characteristic of the murine lung microbiome. To bridge the gap between the lung microbiome and invasive aspergillosis, we investigated the lung microbiome upon its disbalance by an A. fumigatus infection and a possible rebalancing by antifungal treatment. Finally, we aimed to gain the information on the mechanistic basis of potential interactions between lung bacteria and the pathogen.

We could isolate bacteria belonging to 11 species from the lower airways of mice. One of the most prominently isolated bacteria was Ligilactobacillus murinus. We have developed a genetic transformation system for L. murinus to label the bacteria with GFP. We noticed that GFP-labelled L. murinus cells were internalized by murine alveolar epithelial cells. This finding suggests that lung bacteria can be recognized by alveolar epithelial cells, found intracellularly and expected to modulate the immune system of the lung.

Further, we analyzed changes in the lung microbiome upon immunosuppression, infection with A. fumigatus, and antifungal treatment in a mouse model of invasive aspergillosis. Sequencing analysis showed that the composition of the microbiome changed dramatically under all tested conditions. Interestingly, L. murinus was detected in the lungs under all treatments and increased in abundance in the lungs infected with A. fumigatus.To gain insight into potential cause-effect relationships between lung microbiota and a pathogen, isolated bacteria were co-cultivated with A. fumigatus. We found that A. fumigatus promotes growth of L. murinus indicating a direct influence of the pathogen on resident bacteria.