Fig. 6: Comparison between the upper and lower respiratory tract microbiomes.

A Principal Co-ordinates Analysis (PCoA) plot based on JSD of microbial compositions. R² and p values from PERMANOVA are shown. BALF and OP samples from the same individuals were connected with lines. Inserted boxplots show the JSD between different sample types, and different letters on the top indicate statistically significant differences between groups. B 2D density plot showing the correlation of species abundances between BALF and OP. A total of 209 species with relative abundances higher than 0.01 in at least one sample were included. Pearson correlation coefficient and p value are shown. C Volcano plot showing species with differential relative abundances between BALF and OP samples. The horizontal dash line indicates the adjusted p value of 0.05. Differential species are color-coded and labeled with their names. In (A, B), Wilcoxon matched pairs test followed by FDR adjustment was used. D The proportion of OP-BALF-shared species abundance to the total abundance of species. Comparison of the proportion of OP-BALF-shared species between pneumonia and non-pneumonia cases, as per abundance (E) and number (F) of species. In (D–F), only abundant species with relative abundances higher than 0.01 were included. G The relationship between strains detected in the upper and lower respiratory tracts. The number as well as the color and size of dots indicate the number of strains. Symbols on the top indicate the following relationships: strains in BALF were a subset of those in OP, BALF and OP had the same strains, BALF and OP had partially overlapping strains, BALF and OP had completely different strains, strains in OP were a subset of those in BALF. The boxplots on the left indicate the read number of species. In (E–G), asterisks indicate significant differences, *p.adj < 0.05, **p.adj < 0.01, ***p.adj < 0.001, Wilcoxon matched pairs tests. In (A) and (E–G), the center line of the boxplot represents the median, box limits represent upper and lower quartiles, and whiskers represent 1.5x interquartile range. F_ase treated samples were used. n = 34 for BALF and OP.