Fig. 3

The nasal microbiota is less diverse than the peripheral lung microbiota. The Shannon index (a) and Inverse Simpson index (b) were used to assess the alpha diversity of each sample. Each box-and-whiskers plot represents one of the anatomic sites (oral, nasal, bronchial, or lung). The dark horizontal bar represents the median value at each site, while the boxes represent the 25th and 75th percentile values. The whiskers indicate the most extreme (non-outlier) data point that is no more than 1.5 times the interquartile range. Outliers are indicated by circles; Three asterisks indicate p < 0.001 and two asterisks indicate p = 0.01–0.001. The mean ± standard deviation for each site is provided at bottom. Analysis of the Shannon index data (a) indicates that diversity is not identical across groups (Generalized Estimating Equations with a batch effect covariate, p < 0.001). Post hoc comparison using the Holm correction shows that the nasal microbiota is significantly less diverse than all other sites. The oral microbiota is also significantly less diverse than the peripheral lung microbiota. Analysis of the Inverse Simpson index data (b) shows that diversity is not identical across groups (Generalized Estimating Equations with a batch effect covariate, p < 0.001). Post hoc comparison using the Holm correction shows that the nasal microbiota is less diverse than the peripheral lung microbiota (p = 0.02)