Lung microbiota changes during pulmonary Aspergillus fumigatus infection in rats

Since realization that lungs are not sterile, but normally harbor various bacterial species, studies were conducted to define healthy lung microbiota and to investigate whether it changes during lung diseases, infections, and inflammation. Using next generation sequencing we investigated bacterial microbiota from whole lungs in two rat strains (previously shown to differ in gut microbiota composition) in healthy state and during pulmonary infection caused by opportunistic fungi Aspergillus fumigatus. No differences in alpha diversity indices and microbial composition between DA and AO rats prior to infection were noted. Fungal infection caused dysbiosis in both rat strains characterized by increase in alpha diversity indices and unchanged beta diversity. Relative abundance of genera and species was generally increased in DA, but decreased in AO rats during infection. Changes in lung microbiota coincided with inflammation (in both rat strains) and oxidative stress (in DA rats). Disparate response of lung microbiota in DA and AO rats to pulmonary fungal infection might render these two rat strains diffenrentialy susceptible to subsequent inflammatory insult.