Fig. 3

Bacterial and fungal community structure in the nasal and oropharyngeal respiratory niches. a Violin plots representing bacterial load measured by quantitative PCR and bacterial diversity (Shannon index) for samples of the nasal and oropharyngeal habitats. b Corresponding violin plots for fungal amplicon data. c PCoA on the weighted UniFrac distances shown along the first two principal coordinates for bacterial amplicon data. Ellipses represent the 95% confidence interval around the group centroid. d Corresponding PCoA for fungi amplicon data. e Bacterial signature amplicons comparing the nasal and oropharyngeal niches using MaAsLin for Differential Abundance testing (DA) adjusted for sampling and processing variation. Only significant taxa with a p value < 0.05 are shown. f Normalised relative abundance of the top 2 bacterial signature taxa of the nasal and oropharyngeal niches. Boxplots represent the median and interquartile range with whiskers determined by Tukey’s method. g Fungal signature amplicons comparing the nasal and oropharyngeal niches using MaAsLin. h Normalised relative abundance of the top 2 fungal signature taxa of the nasal and oropharyngeal niches. Sample sizes for all panels are n = 78 for nasal habitat bacterial data, n = 105 for oropharyngeal bacterial data, n = 68 for nasal habitat fungal data and n = 44 for oropharyngeal fungal data. Colors are representative of the nasal (grey) and oropharyngeal (orange) samples with grey lines linking samples obtained from the same individual. Statistics represent the result of non-parametric Wilcoxon Rank Sum testing for panels a–b with p value < 0.05, < 0.01 and < 0.001 represented as *, ** and ***, respectively