PXD066865

PXD066865 is an original dataset announced via ProteomeXchange.

Title	Untargeted proteomics of Enterocloster asparagiformis, E. citroniae, E. pacaense treated with DMSO or urolithin M6
Description	Urolithins are a class of bioactive metabolites derived from the metabolism of dietary ellagitannins by the human gut microbiota. In the gut, urolithins are dehydroxylated regioselectively based on microbiota composition and activity. A single 9-hydroxy urolithin dehydroxylase (ucd) operon in gut resident Enterocloster species has been described to date; however, most enzymes in the urolithin metabolic pathway remain uncharacterized. Here, we investigate urolithin cross-feeding between members of the gut microbiota and discover a novel urolithin dehydroxylase in a subset of Enterocloster species. We show that urolithin intermediates, released by gut resident Gordonibacter species during ellagic acid metabolism, are dehydroxylated at both the 9- and 10-positions by E. asparagiformis, E. citroniae, and E. pacaense, but not E. bolteae. Using untargeted proteomics, we uncover a 10-hydroxy urolithin dehydroxylase operon, termed uxd, responsible for these species-specific differences in urolithin metabolism. By inducing uxd expression with diverse urolithins, we show that 9-hydroxy urolithins are required for uxd transcription and 10-position dehydroxylation. Collectively, this study reveals some of the genes, proteins, and substrate features underlying differences in urolithin metabolism by the human gut microbiota.
HostingRepository	PRIDE
AnnounceDate	2025-11-12
AnnouncementXML	Submission_2025-11-12_06:47:36.737.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD066865
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Reilly Pidgeon
SpeciesList	scientific name: Enterocloster citroniae; NCBI TaxID: NEWT:358743; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Enterocloster hominis (ex Hitch et al. 2024); NCBI TaxID: NEWT:1917870; scientific name: Enterocloster asparagiformis; NCBI TaxID: NEWT:333367;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-01 09:24:28	ID requested
⏵ 1	2025-11-12 06:47:37	announced

10.6019/PXD066865;

submitter keyword: microbiome, DMSO, M6, bacteria,Enterocloster, urolithin

Bastien Castagner
contact affiliation	Department of Pharmacology & Therapeutics, McGill University, 3655 Prom. Sir-William-Osler, Montreal, Quebec, H3G 1Y6, Canada. McGill Centre for Microbiome Research, Montreal, Quebec, Canada
contact email	bastien.castagner@mcgill.ca
lab head
Reilly Pidgeon
contact affiliation	Department of Pharmacology & Therapeutics, McGill University
contact email	reilly.pidgeon@mail.mcgill.ca
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/2025/11/PXD066865

PRIDE project URI

• PRIDE
  1. PXD066865
     1. Label: PRIDE project
     2. Name: Untargeted proteomics of Enterocloster asparagiformis, E. citroniae, E. pacaense treated with DMSO or urolithin M6