Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis.
BACKGROUND
Several microbial studies reported gut microbiota dysbiosis in patients with cystic fibrosis (CF). The functional consequences of this phenomenon are poorly understood. Faecal metaproteomics allows the quantitative analysis of host and microbial proteins to address functional changes resulting from this dysbiosis.


METHODS
We analysed faecal protein extracts from fifteen patients with CF that have pancreatic insufficiency and from their unaffected siblings by shotgun proteomics. Novel computational and statistical tools were introduced to evaluate changes in taxonomic composition and protein abundance.


RESULTS
Faecal protein extracts from patients with CF were dominated by host proteins involved in inflammation and mucus formation. Taxonomic analysis of the microbial proteins confirmed the strong reduction of butyrate reducers such as Faecalibacterium prausnitzii and increase of Enterobacteriaceae, Ruminococcus gnavus and Clostridia species.


CONCLUSIONS
Faecal metaproteomics provides insights in intestinal dysbiosis, inflammation in patients with CF and can be used to monitor different disease markers in parallel.
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Griet
G
Debyser
Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281, B-9000 Ghent, Belgium.
Bart
B
Mesuere
Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281, B-9000 Ghent, Belgium.
Lieven
L
Clement
Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281, B-9000 Ghent, Belgium.
Jens
J
Van de Weygaert
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Pieter
P
Van Hecke
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Gwen
G
Duytschaever
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Maarten
M
Aerts
Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281, B-9000 Ghent, Belgium.
Peter
P
Dawyndt
University Hospital of Leuven, Department of Paediatrics, Gasthuisberg Herestraat 49, B-3000 Leuven, Belgium.
Kris
K
De Boeck
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Peter
P
Vandamme
Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
Bart
B
Devreese
D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D003013:Clostridium / Q000302:isolation & purification; D003550:Cystic Fibrosis / Q000150:complications* / Q000382:microbiology; D064806:Dysbiosis / Q000175:diagnosis* / Q000209:etiology / Q000382:microbiology; D004755:Enterobacteriaceae / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology*; D005260:Female; D006801:Humans; D007249:Inflammation / Q000175:diagnosis* / Q000209:etiology / Q000382:microbiology; D008297:Male; D040901:Proteomics / Q000379:methods*
Cystic fibrosis; Dysbiosis; Metaproteomics; Unipept