Fig. 1

A Composition of sputum microbiome was highly explained by dominant taxa and severity of the disease between patients. Principal Coordinate Analysis (PCoA) based on Bray–Curtis dissimilarity between samples. Points are colored by the dominant taxa detected and the shape indicates the phenotype severity based on ppFEV₁. Crosses indicate the centroid of each cluster and the dashed lines the mean distances between clusters. Ellipses represent the 95% confidence interval of intra-cluster variability of sample distance to the centroid. Distances on PCo1 and PCo2 between groups based on dominant taxa were compared by Mann–Whitney U tests with Benjamini–Hochberg correction for multiple testing (Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1). Cluster of Staphylococcus dominated samples were significantly different to clusters with Pseudomonas and Streptococcus dominated microbiomes on PCo1 and PCo2. B Changes in sputum microbiome composition within patients between visits. A shift of dominance between Staphylococcus to Stenotrophomonas was linked to a high Bray–Curtis dissimilarity between visits for patient 9 (P9). For panel B and E each color represents samples from the same patient. C Association of dominant genera to alpha-diversity measures in sputum microbiomes. D Heatmap of the most abundant genera (> 0.5% mean relative abundance) for each cluster of dominant taxa observed on panel A). Dendrogram indicates Ward clustering of samples. E Relationship between dominant taxa in sputum and lung function. Lung function is represented by ppFEV1 at each visit, points are colored by patient and the size represents the relative abundance in percentage at the sample. Dashed read line indicates the threshold of 70% ppFEV1 to separate moderate (< 70%) from mild (> 70%) severity