Griet Debyser

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The human gut microbiome is a diverse and complex microbial ecosystem. In patients with cystic fibrosis (CF) this microbiome is influenced drastically due to antibiotic treatments, the enlarged mucus layer in the small intestine and the different alimentary environment due to decreased release of digestive enzymes by the pancreatic duct. These problems not only entail changes in the composition of the gut microbiome (dysbiosis), but also cause intestinal inflammation and affect the general well-being of patients with CF.

A shotgun metaproteomics approach (gel-LC-ESI-FT-MS/MS) is used to characterize and compare the predominant members of the intestinal microbiome of a group of patients with CF and their siblings. Faecal protein extracts were separated by 1D SDS-PAGE and in-gel digested. The tryptic peptides were separated on a 1D LC system and on-line measured on a LTQ-FT Ultra mass spectrometer. The characterization of the predominant members of the intestinal microbiota was performed using Unipept (, a novel approach for identifying taxon-specific peptides. 

We found evidence for a metaproteomic difference in the gut microbiome of patients with CF and their siblings. Bacteria of the phylum Firmicutes, and in particular butyrate-producing bacteria belonging to Clostridium clusters IV and XIVa were underrepresented in patients with CF. Furthermore a differentially expressed protein study shows that proteins of the butyrate synthesis pathway are less abundant in the faecal microbiome of CF patients.