Fig. 3

Bacterial communities in murine whole lung tissue have increased alpha diversity relative to BAL fluid and negative controls. a Whole lung tissue contains a greater number of unique bacterial taxa than BAL fluid and negative controls. Richness of the bacterial community in each tissue or control specimen was determined by clustering reads with species-level similarity (≥ 97% sequence identity) into operational taxonomic units (OTUs) and calculating the number of unique OTUs within each specimen, normalized to 100 reads per specimen to account for variation in sequencing depth. Mean ± SEM and individual data points are shown. Pairwise significance was determined by comparing whole lung tissue and BAL fluid to pooled sampling, isolation, and sequencing controls (respectively, as shown) using Tukey’s Honest Significant Difference (HSD) test. Significance key: ns p > 0.05; *p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001