Dataset Information

Metaproteomic profiling of induced and spontaneous sputum samples from cystic fibrosis patients

ABSTRACT: Application of a mass spectrometry -based approach to assess the lung microbiota composition and the associated metaproteomic functionality of subjects with cystic fibrosis

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Archaea Bacteria Viruses Eukaryota (eucaryotes)

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD034628 | Pride | 2023-02-04

REPOSITORIES: pride

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Quick and wide-range taxonomical repertoire establishment of the cystic fibrosis lung microbiota by tandem mass spectrometry on sputum samples.

Hardouin Pauline P Pible Olivier O Marchandin Hélène H Culotta Karen K Armengaud Jean J Chiron Raphaël R Grenga Lucia L

Frontiers in microbiology 20221013

Microorganisms proteotyping by tandem mass spectrometry has been recently shown as a powerful methodology to identify the wide-range taxonomy and biomass of microbiota. Sputum is the recommended specimen for routine microbiological monitoring of Cystic Fibrosis (<i>CF</i>) patients but has been rarely submitted to tandem mass spectrometry-based proteotyping. In this study, we compared the microbial components of spontaneous and induced sputum samples from three cystic fibrosis patients. Although ...[more]

PMID: 36312921

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Project description:Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo - an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.

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