Figure 3

Microbial communities cluster by patient, not by clinical stage. (A) Hierarchical clustering of top 12 genera found in patient samples. Each clinical BETR stage is designated by color (baseline, green; exacerbation, red; treatment, orange; recovery, blue) along the top of the diagram; patient number is given across the bottom. The relative abundance for each genus is colored in shades of red (low relative abundance) to yellow or bright white (high relative abundance) as shown in the color key (upper left). The x-axis of the color key (row Z-score) indicates the number of standard deviations from the mean relative abundance for each genus. The count histogram indicates the mean counts for all data in sample set. (B) Principal coordinate analysis of all patients. Clinical stages are represented by colored dots (baseline, green; exacerbation, red; treatment, orange; recovery, blue) and black lines connect the trajectories of each patient’s microbiome throughout the study. BETR, baseline, exacerbation, treatment and recovery.