Fig. 3.

Analysis of lung microbiome. a OTU count and (b) Inverse Simpson index in samples rarefied to even sequencing depth. c Multidimensional scaling analysis of samples as indicated with ellipses indicating 80% confidence of sample distribution. d Plots showing log normalised relative abundance of the 6 most abundant bacterial phyla. e Multidimensional scaling analysis of lung microbiomes from groups as indicated, with ellipses indicating 80% confidence of sample distribution. f Composition of lung microbiome grouped by phylum for individual animals. All symbols, statistical tests and significance levels as in Fig. 1