PXD025134

PXD025134 is an original dataset announced via ProteomeXchange.

Title	A combined metaproteomics and metabolomics approach for the in vivo analysis of cystic fibrosis sputum focusing on microbial pathogens
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 paves the way for the colonization by microbial pathogens and the concomitant establishment of chronic infections leading to lung tissue damage, reduced lung function, and to decreased life expectancy. Although microbial infections play a key role during disease progression, only a few studies investigated the pathophysiology of the microbial community in vivo so far. Moreover, no CF study so far applied metaproteomics, a powerful approach to unravel molecular mechanisms of microbial infection, mainly reasoned due to (I) the challenging processability of inhomogeneous, viscous, slimy sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. Consequently, we developed a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, and subsequent metaproteomics analyses with a focus on microbial pathogens overcoming the aforementioned challenges. Metaproteomics data were complemented and validated by 16S sequencing, metabolomic as well as microscopic analyses. In total, we processed 21 CF sputum samples and selected three for detailed metaproteome analysis. The number of bacterial proteins/protein groups increased from 199-425 to 392-868. Moreover, our data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera are so far 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 against mucoviscidosis.
HostingRepository	PRIDE
AnnounceDate	2021-11-03
AnnouncementXML	Submission_2021-11-03_03:19:09.402.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniela Zuehlke
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-31 11:08:21	ID requested
⏵ 1	2021-11-03 03:19:10	announced

Graf AC, Striesow J, Pan, é, -Farr, é J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, Riedel K, An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum. Front Cell Infect Microbiol, 11():724569(2021) [pubmed]

submitter keyword: Cystic fibrosis, sputum, microbial community, microbiome, 16S sequencing, metaproteomics, metabolomics, in vivo

Katharina Riedel
contact affiliation	University of Greifswald, Institute of Microbiology, Department of Microbial Physiology & Molecular Biology
contact email	riedela@uni-greifswald.de
lab head
Daniela Zuehlke
contact affiliation	University of Greifswald, Institute of Microbiology
contact email	zuehlke@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/11/PXD025134

PRIDE project URI

• PRIDE
  1. PXD025134
     1. Label: PRIDE project
     2. Name: A combined metaproteomics and metabolomics approach for the in vivo analysis of cystic fibrosis sputum focusing on microbial pathogens