PXD015215

PXD015215 is an original dataset announced via ProteomeXchange.

Title	Stable Isotope Probing Deuterium LC-MS/MS
Description	Competition between commensal and pathogenic microbes for monosaccharides derived from mucus layer O-glycans as nutrient sources has been proposed as a mechanism by which the gut microbiota counteracts pathogen colonization. However, our understanding of the microbial interactions that determine competition for these sugars in complex microbial communities, and how to exploit such information to develop therapies, is limited. Here, we employed heavy water (D2O)-based activity labeling followed by automated Raman-Activated Cell Sorting of active (D-labeled) cells and metagenomics to identify mouse gut commensals that forage on O-glycan monosaccharides. Sequencing of cell-sorted fractions revealed members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae and Bacteroidaceae families. We further show that the ability of these organisms to forage on mucosal sugars is well-supported by the presence of partial or complete catabolism pathways for O-glycan utilization in their genomes. Remarkably, administration of a 5-member bacterial consortium based on identified sialic acid and N-acetylglucosamine utilizers results in limited access of the gut pathogen Clostridioides difficile to mucosal sugars and in impaired pathogen colonization of antibiotic-treated mice. Our findings underscore the value of using targeted approaches to identify organisms performing key functions in the gut and to rationally design effective probiotic mixtures.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:12:10.429.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-29 05:37:16	ID requested
1	2020-09-09 06:44:41	announced
2	2020-10-19 01:01:05	announced	2020-10-19: Updated publication reference for PubMed record(s): 33037214.
⏵ 3	2024-10-22 05:12:13	announced	2024-10-22: Updated project metadata.

Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D, Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization. Nat Commun, 11(1):5104(2020) [pubmed]

10.1038/s41467-020-18928-1;

submitter keyword: Stable isotope probing, nutrient competition, mucosal sugars, colonization resistance, metaproteomics

Nico Jehmlich
contact affiliation	Department Molekulare Systembiologie Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Permoserstraße 15 04318 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.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/2020/09/PXD015215

PRIDE project URI

• PRIDE
  1. PXD015215
     1. Label: PRIDE project
     2. Name: Stable Isotope Probing Deuterium LC-MS/MS