Figure 2

Relative abundance of top twelve genera. (A) Stacked bar charts of relative abundance (left y-axis) of the top 12 genera for each patient across a clinical exacerbation show that 12 genera explain 90% of the complexity for all patient samples. (B) Relative abundance of the top 12 genera are plotted against the prevalence of each genus in the nine complete (BETR, BER) patient samples and show that bacteria that are highly abundant in a single patient are also highly prevalent across patients. The colored dots indicate those genera that are both highly abundant and highly prevalent, and the colors correspond to the legend shown in panel A. Colors in panels A and B correspond to genera as indicated by the legend beneath panel A. (C) The fraction of P. aeruginosa determined by qPCR (rplU detection/16s rRNA detection) correlates to the fraction of deep-sequencing reads assigned to the Pseudomonas genus. qPCR samples were analyzed six times and the median fraction values for each sample are shown. There is one outlier in this dataset (sample 206R, shown in red). When this outlier is removed from the analysis, the linear regression slope is 1.1 and R² = 0.90. BER, baseline, exacerbation and recovery; BETR, baseline, exacerbation, treatment and recovery; qPCR, quantitative PCR.