The murine lung microbiome is dysbalanced by the human pathogenic fungus Aspergillus fumigatus resulting in enrichment of anaerobic bacteria

Here, we report significant changes in the composition of the lung microbiome and metabolome of mice under immune suppression, infection of immunosuppressed mice with virulent and avirulent strains of the clinically important human-pathogenic fungus Aspergillus fumigatus, and treatment with the clinically used antifungal drug voriconazole. Our data also indicate the important role of the gut microbiome for the lung homeostasis mediated by the plasma metabolome. In the lung microbiome, infection by A. fumigatus led to a significant increase of anaerobic bacteria, most prominently of Ligilactobacillus murinus. We also isolated live bacteria including L. murinus from the murine lower respiratory tract. In vitro, L. murinus is tolerated and even internalized by alveolar epithelial cells. Co-cultivation of L. murinus and A. fumigatus led to a reduction in oxygen concentration accompanied by an increase of L. murinus cells suggesting that A. fumigatus establishes a microaerophilic niche, thereby promoting growth of anaerobic bacteria.