Table 1.
Patients’ characteristics.
Fig 1.
Descriptive analysis of the sequencing reads.
(A) Distribution of the number of reads over the whole dataset. (B) Number of samples with detection of the indicated percentage of the microbiome at the genus level by culture. Strains isolated by culture were classified at the genus level and correspondence with the NGS dataset was analyzed.
Fig 2.
Relative abundance of the bacterial genera depending on the sampling site.
The colored segments of each bar represent the proportion of reads mapping to different bacterial genera.
Fig 3.
Alpha-diversity of the upper and lower airways microbiomes from clinically stable children with CF.
Alpha-diversity was calculated with the non parametric Shannon index (A), richness was estimated with the Chao1 estimate (B) and evenness was calculated based on the Shannon index (C). Alpha-diversity variation among nose, throat and sputum microbiome was analyzed with a linear mixed model with random effects for CF patients and paired comparisons were done with a Tukey post-hoc test for pairwise comparison.
Fig 4.
Correlation between alpha-diversity and bacterial load in CF airways.
The alpha-diversity is represented by the non parametric Shannon index (A) and the evenness index based on the Shannon index (B). The microbial load was measured via the proxy of the number of 16S genes. Samples from the three sampling sites are represented.
Fig 5.
Spatial analysis of the airways microbiome.
Nasal swabs are represented by black dots, throat swabs by red dots, sputum samples by green dots. (A) Principal Component Analysis of samples obtained from clinically stable children with CF. In panel (B) samples from patients during exacerbation were added. Pearson correlations were performed to highlight which OTUs were responsible for the divergence among the samples. Correlation was considered significant when the coefficient of correlation was higher than 0.6 and p-value < 0.01. (C) Principal Coordinates Analysis was performed on samples obtained from clinically stable CF patients or (D) on all available samples from CF patients irrespective of the clinical status.
Table 2.
Differential abundance of the most abundant OTUs among the different sampling sites.
Fig 6.
Principal Component Analysis of sputum samples from children and adult patients CF patients.
Sputum samples from children with CF are represented by red points and adult CF patients by blue (at the time of admission in the clinic) and green points (after antibiotics treatment). Pearson correlations were performed to highlight which genera were responsible for the divergence among the samples. Correlation was considered significant when the coefficient of correlation was higher than 0.6 and p-value < 0.01.
Fig 7.
Differential mean raw abundance of Pseudomonas aeruginosa between the two ecotypes of sputum samples.
Mean raw abundance of Pseudomonas aeruginosa in sputum samples from both ecotypes are represented by the raw numbers of reads in the sample. Statistical differences were assessed by a Wilcoxon test.