PXD031457

PXD031457 is an original dataset announced via ProteomeXchange.

Title	Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease
Description	Patients with Parkinson’s disease (PD) exhibit differences in their gut microbial community compared to healthy subjects. Although alterations have been most commonly described as differential abundance of bacteria, fewer studies have focused on the functionnal aspect of these changes. Causal and mechanistic connections between the gut microbiome and PD pathogenesis remain elusive, but could include molecules that influence inflammation or neuronal α-synuclein aggregation. Here, we perform an integrated multi-omic analysis of fecal samples from patients with PD or a prodrome thereof (idiopathic REM sleep behaviour disorder, iRBD) compared to healthy controls. We reveal 11 metabolites significantly different between the three groups, amongst which β-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. In addition, we identified a decrease in transcript for motilty and flagellar assembly pathways in keystone bacteria such as Roseburia and Agathobacter. Our study highlights the apparent disruption of microbial gene expression in PD, in particularly gene associated to mobility which can impact the immune system, and the neuro-inflammation involved in PD.
HostingRepository	PRIDE
AnnounceDate	2025-10-13
AnnouncementXML	Submission_2025-10-12_16:03:57.440.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD031457
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Benoit Kunath
SpeciesList	scientific name: human gut metagenome; NCBI TaxID: NEWT:408170;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-05 13:35:20	ID requested
⏵ 1	2025-10-12 16:03:58	announced

10.1186/s40168-025-02227-2;

Villette R, Ort, í, s Sunyer J, Novikova PV, Aho VTE, Petrov VA, Hickl O, Busi SB, De Rudder C, Kunath BJ, Heintz-Buschart A, Trezzi JP, Halder R, J, ä, ger C, Lebrun LA, Daujeumont A, Schade S, Janzen A, Jehmlich N, von Bergen M, Laczny CC, May P, Trenkwalder C, Oertel W, Mollenhauer B, Wilmes P, Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease. Microbiome, 13(1):200(2025) [pubmed]

10.6019/PXD031457;

submitter keyword: Microbiome

Human

Parkinson

Archaea

Paul Wilmes
contact affiliation	Luxembourg Centre for Systems Biomedicine, University of Luxembourg, University of Luxembourg, Campus Belval, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
contact email	paul.wilmes@uni.lu
lab head
Benoit Kunath
contact affiliation	North Carolina State University
contact email	benoit.j.kunath@gmail.com
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/2025/10/PXD031457

PRIDE project URI

• PRIDE
  1. PXD031457
     1. Label: PRIDE project
     2. Name: Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease