Genome-wide analysis of whole-lung and alveolar macrophages before and after gut microbiome depletion

Pneumonia accounts for more deaths than any other infectious disease worldwide. The intestinal microbiota has emerged as a key defense system by local support of mucosal immunity as well as proposed modulatory effects on systemic immunity. We here investigated the transcriptomes of whole-lungs and alveolar macrophages between untreated and antibiotic treated mice. Broad spectrum antuibiotics were used to deplete the gut microbiome of C57BL6 mice. Whole lungs and alveolar macrophages were isolated and differential gene expression analysis was performed on untreated and antibiotic treated samples.