Fig. 6.

Dynamic changes in oropharyngeal microbiota induced by cigarette smoke and S. pneumoniae . (a) Richness, (b) Shannon’s diversity index and (c) mean relative abundance of bacterial genera are shown for CTRL and SMK groups at the indicated time points relative to pneumococcal infection (see the experimental scheme in Fig. 1a). (a, b) Box-plots indicate median and interquartile range with mean indicated as + and with outliers shown. (c) Abundance of bacterial genera identified by 16S rRNA sequencing at each time point show the mean relative abundance for CTRL (C) and SMK (S) at the indicated time points. Data were analysed by one-way ANOVA (** P <0.01). (d) Hierarchical clustering analysis of the microbial composition. The mean of the relative abundances of the SVs per sample group has been calculated and the DM created. The dendrogram is based on the DM of all SVs, while the heatmap only visualizes SVs with at least 1 % relative abundance in the respective sample group. All data are from 20 to 24 mice per group sampled longitudinally. SVs are named at the genus level. Staph., Parabact., and Enteract indicate Staphylococcus , Parabacteroides and Enteractinococcus , respectively. $Bacteroidales includes all families of the order except Bacteroidaceae , which is shown separately.