Total colony count, aerobic colony count and anaerobic colony count of bacteria in sputum from CF patients and control subjects.

<p>(Median).</p

Relationship between colony count of anaerobic bacteria and CRP.

<p>Relationship between colony count of anaerobic bacteria and CRP.</p

Relationship between anaerobic and aerobic colony count and LCI in CF patients with a) chronic <i>P. aeruginosa</i> infection and b) without <i>P</i>. <i>aeruginosa</i> infection.

<p>Relationship between anaerobic and aerobic colony count and LCI in CF patients with a) chronic <i>P. aeruginosa</i> infection and b) without <i>P</i>. <i>aeruginosa</i> infection.</p

Relationship between FEV₁ z-score and a) total colony count b) aerobic colony count and c) anaerobic colony count.

<p>Relationship between FEV₁ z-score and a) total colony count b) aerobic colony count and c) anaerobic colony count.</p

Relationship between LCI and a) total colony count b) aerobic colony count and c) anaerobic colony count.

<p>Relationship between LCI and a) total colony count b) aerobic colony count and c) anaerobic colony count.</p

CF patient and healthy control subject characteristics.

<p>^aOral and/or inhaled anti-pseudomonal</p><p>CF patient and healthy control subject characteristics.</p

Relative abundance of the bacterial genera depending on the sampling site.

<p>The colored segments of each bar represent the proportion of reads mapping to different bacterial genera.</p

Patients’ characteristics.

<p>BMI, body mass index; FEV1% pred, forced expiratory volume in 1 second % predicted; LCI, lung clearance index, SDS standard deviation score</p><p>Patients’ characteristics.</p

Alpha-diversity of the upper and lower airways microbiomes from clinically stable children with CF.

<p>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.</p

Descriptive analysis of the sequencing reads.

<p>(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.</p