Figures
- FIGURE 1
a) Taxa diversity (Shannon–Wiener diversity index) and b) taxa richness (counts of observed taxa per sample) for the 13 cohorts. Data are presented as intracohort spread with the horizontal line showing median values. Differences between pairs were evaluated using the Mann–Whitney test with Bonferroni adjustment (p<0.05 denoted significant differences). BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash; SAL: saliva; BM: buccal mucosa; HP: hard palate; TD: tongue dorsum; AKG: attached keratinised gingiva; SupP: supragingival plaque; SubP: subgingival plaque; TH: throat; PT: palatine tonsils; AN: anterior nares.
- FIGURE 2
Overall taxa distribution (occupancy) within the 13 cohorts included in the study. The blue dotted line represents a cut-off for taxa termed as “Generalists” determined according to specific operational taxonomic units (sequence types) observed in ≥70% of all samples.
- FIGURE 3
Biplot of principal components analysis conducted for the total community data set (sites and taxa). Per cent variation covered by each principal component is indicated in parentheses in the axis titles, with the first two components accounting for 75.77% total variance explained. Arrows indicate direction and magnitude of loadings (sites) on the first principal component. Factors and taxa names that had limited effect on any of the sites (i.e. clustered near the centre axis) are displayed as their assigned rank number for clarity. BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash; SAL: saliva; BM: buccal mucosa; HP: hard palate; TD: tongue dorsum; AKG: attached keratinised gingiva; SupP: supragingival plaque; SubP: subgingival plaque; TH: throat; PT: palatine tonsils; AN: anterior nares.
- FIGURE 4
Unweighted UniFrac principal coordinate analysis (PCoA) plots illustrating the relationship between the bacterial diversity in samples from the current study. a) All 13 cohorts, b) V1V3 versus V1V2 overlapping primer pairs and c) geographical sampling location. BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash.
- FIGURE 5
Microbial co-occurrence network for the main taxa from a) 13 sites of the greater airways (taxa accounting for >0.5% of the total sequences in the 778 samples of the combined upper airways), b) co-occurring microbial taxa from the cystic fibrosis (CF) subset (taxa >0.1% of total sequences), c) co-occurring microbial taxa from the bronchiectasis subset (taxa >0.1% of total sequences), and d) co-occurring microbial taxa from the CF mouthwash subset (taxa >0.1% of total sequences). Each node denotes a particular taxon within the network and each line (edge) a significant co-occurrence relationship (Spearman's rank correlation coefficient >0.5 for positive correlations (blue lines) and <−0.5 for negative correlations (red lines); adjusted p-value <0.005 (false discovery rate correction for multiple testing according to the Benjamini–Hochberg–Yekutieli procedure). Nodes are coloured according to “Generalists” (blue), “Chronic Airways Disease Specialists” (red), “Niche Associated” (green) and not belonging to any of the former three groups (aqua).
Tables
- TABLE 1
Sample numbers studied for each cohort included in this study
Collection site Cohort Samples Anterior nares Healthy 67 Attached keratinised gingiva Healthy 102 Subgingival plaque Healthy 92 Supragingival plaque Healthy 103 Saliva Healthy 69 Hard palate Healthy 93 Tongue dorsum Healthy 99 Buccal mucosa Healthy 98 Throat Healthy 94 Palatine tonsils Healthy 97 Cystic fibrosis sputum Disease 94 Cystic fibrosis mouthwash Disease 23 Bronchiectasis sputum Disease 26 Total 1057
Supplementary Material
Please note: supplementary material is not edited by the Editorial Office, and is uploaded as it has been supplied by the author.
FIGURE S1 00128-2017.figureS1
FIGURE S2 00128-2017.figureS2
FILE S1 00128-2017.fileS1
FILE S2 00128-2017.fileS2
Detailed methods 00128-2017.supp
TABLE S1 00128-2017.tableS1
TABLE S2 00128-2017.tableS2
TABLE S3 00128-2017.tableS3
TABLE S4 00128-2017.tableS4
TABLE S5 00128-2017.tableS5
