Microbiological data from CF patients included in the study.

a<p>DE, direct examination;</p>b<p>Nested PCR was used to identify <i>Pneumocystis jirovecii</i> colonization <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone.0036313-MontesCano1" target="_blank">[26]</a>;</p>c<p>rt-PCR, real-time polymerase chain reaction assay to detect <i>Aspergillus fumigatus</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone.0036313-Fralle1" target="_blank">[27]</a>;</p>d<p>ND, not done;</p>e<p>PH, Pseudo-hyphae and H, hyphae.</p

Rarefaction curves.

<p>These curves are representing the numbers of OTUs with respect to the number of pyrosequence reads obtained from each patient at different sampling times and using the two set of primers targeting prokaryotic 16S rDNA (A) and fungal ITS2 (B) loci.</p

Number of ITS-pyrosequencing reads assigned to each taxonomic group of Fungi.

a<p>Once a read was assigned to the highest taxonomical level according to the criteria defined in material and method section, it was not added up in the next taxonomic level.</p

Relation between species richness and clinical status (A) or lung function (B).

<p>Total richness of prokaryotic and fungal communities from each patient-sample was expressed using the Chao1 richness estimator; each spot size is proportional to the corresponding Chao1 value. The clinical status is expressed as S-K score and BMI in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone-0036313-g002" target="_blank">Figure 2A</a>, while lung function is expressed as FEV1 and FVC values in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone-0036313-g002" target="_blank">Figure 2B</a>. Given to the absence of S-K score value from Patient 2-sample 2 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone-0036313-t001" target="_blank">Table 1</a>), this spot is missing in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036313#pone-0036313-g002" target="_blank">Figure 2A</a>. Bacterial and fungal Chao1 values corresponding to Patient 1, Patient 2, Patient 3, and Patient 4 are represented in blue-, green-, red- and yellow-edged spots, respectively. Dark and light colour intensity is corresponding to the first and second sampling dates of each patient, respectively. Dark grey and light grey are corresponding to fungal and bacterial Chao1 richness values, respectively.</p

Clinical data and treatment from CF patients included in the study.

a<p>S-K score, Shwachman-Kulczycki Score;</p>b<p>BMI, body mass index;</p>c<p>FVC, forced vital capacity;</p>d<p>FEV1, forced expiratory volume;</p>e<p>ATB, antibiotic drug;</p>f<p>ATF, antifungal drug;</p>g<p>ITC, itraconazole;</p>h<p>UNK, unknown CFTR mutations associated with an abnormally high sweat chloride test (110 mmol/L).</p

Number of 16S-pyrosequencing reads assigned to each taxonomic group of Bacteria.

a<p>Once a read was assigned to the highest taxonomical level according to the criteria defined in material and method section, it was not added up in the next taxonomic level.</p