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Fig. S1. Correspondence analysis (CA) plot: relatedness of BAL and oropharyngeal bacterial communities identified by the PhyloChip (pairs indicated by the same colour; square BAL and circle oropharyngeal sample). Black circles represent all oropharyngeal bacterial community from 45 children with CF. This analysis reveals that lower CF respiratory tract (sampled using BAL) and upper respiratory tract bacterial communities (sampled using oropharyngeal swab) from the same patient, sampled at the same time, generally group together. Each circle represents one community from one child. The percentages of variation described by the correspondence analysis coordinates are shown in parentheses.

Fig. S2. A. Diversity as measured by Shannon index (H) averaged across participants of the same age plotted against age. B. Evenness [Shannon index (H)/natural log(species richness)] averaged across participants of the same age plotted against age. C. Phylogenetic diversity within each community (alpha diversity) averaged across participants of the same age plotted against age. Here phylogenetic diversity within individual communities was measured as the mean pair-wise phylogenetic distance (MPD) separating randomly drawn pairs of microbial taxa occurring in that community (8).

Fig. S3. A phylogenetic tree of cumulative bacterial taxa from all samples whose abundance changed significantly based on P. aeruginosa or antibiotic presence/absence was constructed in ARB using parsimony. Coloured boxes represent the following, with darker hue indicating an increase and lighter a decrease: blue for P. aeruginosa, red for oral antibiotics and green for inhaled antibiotics. Only taxa/species that changed by > 10-fold (t-test with q-value < 0.01) between the groups were plotted.

Fig. S4. Average frequency of bacterial taxa/species in communities that were negative (top) and positive for P. aeruginosa by culture (bottom). Peaks with average frequency greater than 0.05% were: (1) Synergistes unknown (AF229792.1), (2) Fusobacterium unknown (AY274839.1), (3) unknown Chloroflexi bacterium (AJ306793), (4) Cyanobacterium sp. (X82156.1), (5) uncultured Chromatiales (AJ518784.1), (6) Pasteurellaceae group (AB088998.1), (7) Helicobacter group, (8) Micrococcae group, (9), (10) and(11) Clostridiales, (12) Streptococcus group (AF009482.1), (13) Clostridium sp. unclassified, (14) Rihanellaceae, (15) Prevotellaceae group (AF371893.1), (16) Xanthomonas (AB110496), (17) Pseudomonadeaceae (AE004501.1), (18) Pseudoalteromonas ruthenica (AF316891.1), (19) Staphylococcae group, (20) Streptococcus constellatus (AF104676.1) and Streptococcus gordonii (AF003931.1). An average frequency of 0 indicates there was no change in taxon presence with and without P. aeruginosa.

Table S1. Overview of enrolled study subjects by age, CF genotype and FEV1.

Table S2.T-test for bacterial taxa/species that varied significantly (q-value < 0.01 and > 10-fold change) between communities that had culture-proven P. aeruginosa and those that were culture-negative for P. aeruginosa. Taxa ordered by fold change starting with greatest.

Table S3.T-test for bacterial taxa/species that varied significantly (q-value < 0.01 and > 10-fold change) between communities currently exposed to oral antibiotics and those that were not. Taxa ordered by fold change starting with greatest.

Table S4.T-test for bacterial taxa/species that varied significantly (q-value < 0.01 and > 10-fold change) between communities currently exposed to inhaled tobramycin (TOBI) and those that were not. Taxa ordered by fold change starting with greatest.

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