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

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

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

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

Main clinical characteristics of COPD patients switching of Clusters between visit 1 and visit 2.

(PDF)</p

Changes in the serum levels of the significantly-regulated proteins between COPD patients from Cluster 1 and Cluster 2.

(PDF)</p

Biological classification of the top 90 proteins enriched in Cluster 2 COPD patients.

Biological classification of the top 90 proteins enriched in Cluster 2 COPD patients.</p

Two COPD patient Clusters show differentially expressed proteins enriched for distinct biological pathways.

(A) Volcano plot showing differentially expressed proteins between Cluster 1 and Cluster 2. X axis corresponds to log2 (fold change) and Y axis corresponds to -log10 (FDR). Yellow indicates proteins with significant downregulation and blue indicates those with significant upregulation (Fold change >1.5 and FDR versus Cluster 1, regrouped in three core functions defined as “Immunity and defense”, “Cell fate, repair and remodeling”, and “Metabolism and mitochondria”.</p