Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis  Griet Debyser, Bart Mesuere, Lieven Clement, Jens Van de Weygaert, Pieter Van Hecke, Gwen Duytschaever, Maarten Aerts, Peter Dawyndt, Kris De Boeck, Peter Vandamme, Bart Devreese  Journal of Cystic Fibrosis  Volume 15, Issue 2, Pages 242-250 (March 2016) DOI: 10.1016/j.jcf.2015.08.003 Copyright © 2015 European Cystic Fibrosis Society. Terms and Conditions

Fig. 1 Taxonomic composition of the faecal microbiota in the patients with CF and in the unaffected siblings based on average relative spectral counts assigned to phylum (A) and genus (B). Coloured blocks indicate taxa with an average relative abundance >1% in at least the sibling or the patients. The remaining taxa were binned as ‘other’ along with the fraction of peptides that could not be assigned at the taxa level ‘unclassified’ (uncl.). Journal of Cystic Fibrosis 2016 15, 242-250DOI: (10.1016/j.jcf.2015.08.003) Copyright © 2015 European Cystic Fibrosis Society. Terms and Conditions

Fig. 2 Changes of the relative abundance of Enterobacteriaceae (A), Ruminococcus gnavus (B) and Faecalibacterium prausnitzii (C) in patients with cystic fibrosis. The left panels display raw ratios of spectral counts for each taxon on the total bacterial spectral counts in unaffected siblings (sib) and patients with CF (CF). The right panels visualise log transformed raw ratios (dots) along with the zero inflated negative binomial (ZINB) model fit (thick lines) for siblings in black and for patients in red. Patient–sibling pairs are connected with lines. The raw ratios indicate that Enterobacteriacea and R. gnavus typically have a higher prevalence in the faecal microbiota of CF patients compared to their corresponding siblings, while the reverse is true for F. prausnitzii. The ZINB model confirms this. The regression lines in the plot represent the average logged relative abundance for siblings (black) and patients (red) in function of age. The difference between the lines represents the effect of CF after correcting for age, which was highly significant (q=0.001 and q=0.005, respectively). Journal of Cystic Fibrosis 2016 15, 242-250DOI: (10.1016/j.jcf.2015.08.003) Copyright © 2015 European Cystic Fibrosis Society. Terms and Conditions