Fig 1.
Illustration of the combinations of upper and lower airway samples taken.
Forty-nine patients were recruited and in forty-seven patients, a throat swab and at least 1 lower airway sample was obtained for comparison. Samples for forty-two patients remained after rarefying to 1000 reads: 8 patients remained in whom all 4 samples were available; 39 had TS and at least a paired lower airway sample (either BALF, bronchial brushing or both), and 17 had CS and a paired lower airway sample. n—number of subjects. After rarefaction, some subjects had fewer samples for comparison and therefore moved into a different category.
Table 1.
Summary of patient characteristics (n = 49) in the comparison of the upper and lower airway microbiota.
CSLD—chronic suppurative lung disease; CF—cystic fibrosis; NBS—newborn screened; PCD—Primary ciliary dyskinesia.
Fig 2.
Heatmap showing similarities in the relative abundances of the top 50 OTUs present between upper (throat swabs [TS] and cough swabs [CS] and lower airway samples (bronchoalveolar lavage fluid [BALF] and bronchial brushings).
Fig 3.
Individual patient barplots (N = 39) comparing paired lower airway samples and TS for the 50 most common OTUs.
The relative abundance of OTUs for each sample is shown with TS below and their corresponding lower airway sample above. Bars are of uneven heights due to the presence of low abundance “other” OTUs which have not been included in the plot. This illustrates that the airway microbiota is highly individual with variable degrees of similarity between TS and lower airway samples.
Fig 4.
Alpha-diversity comparisons between lower airway samples and throat swabs.
No significant difference was seen in: (a) richness (t(38) = 1.6523, P = 0.107); (b) evenness (W(38) = 367, P = 0.756), and (c) Shannon diversity index (W(36) = 384, P = 0.940).
Fig 5.
Non-metric multidimensional scaling (NMDS) plot comparing the UniFrac score between patients.
This shows similarity in the clustering pattern between lower airway samples and throat swabs.
Table 2.
Comparing the mean relative abundance (percent) of the most common or clinically important genera between TS and paired lower airway samples (BALF or bronchial brushing).
Using multiple paired t-tests with Benjamini-Hochberg correction, only Streptococcus spp. was significantly different (P(adj) = 0.0009). TS—throat swab; NS—non-significant (P(adj) > 0.05). SD—standard deviation.
Table 3.
Beta diversity summaries of significant clinical variables influencing community structure.
Adonis (PERMANOVA) results shown are for those variables which were statistically significant (P < 0.05) using the Bray Curtis dissimilarity score. IV—intravenous. FOB—fibreoptic bronchoscopy.