PXD056968

PXD056968 is an original dataset announced via ProteomeXchange.

Title	Systematic Metaproteomic Mapping of Ex vivo Gut Microbiota Functional Responses to Therapeutic Drugs (3)
Description	Some therapeutic compounds can influence our gut microbiota, but a comprehensive understanding of their impact on microbial systems ecology remains largely unexplored. This study examines the impact of 312 therapeutic compounds on metaproteomes of six ex vivo human gut microbiota, generating 4.6 million microbial protein responses, available as an interactive resource. Further data analysis discovered that 15% of the compounds induced consistent functional changes across microbiotas, with neuropharmaceuticals being significantly enriched. These neuropharmaceuticals induced profound metaproteomic alterations, along with community-level functional redundancy (FR) decrease and antimicrobial resistance protein (ARP) increase. Two functional states in the metaproteomic response landscape were observed: one with high FR and low ARP, and another with decreased FR and induced ARP. Based on the energy landscape principle, we validated that enhancing FR maintained a microbiota’s resilience against neuropharmaceutical-induced ARP increase. Our results highlight a novel strategy to counter drug-induced negative impacts by leveraging the functional landscape.
HostingRepository	PRIDE
AnnounceDate	2025-08-28
AnnouncementXML	Submission_2025-08-27_19:02:11.638.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leyuan Li
SpeciesList	scientific name: human gut metagenome; NCBI TaxID: 408170;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-19 06:42:51	ID requested
⏵ 1	2025-08-27 19:02:12	announced

Dataset with its publication pending

submitter keyword: Gut microbiota, microbiome, drug response, functional redundancy, metaproteomics

Daniel Figeys
contact affiliation	Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
contact email	dfigeys@uottawa.ca
lab head
Leyuan Li
contact affiliation	National Center for Protein Sciences, Beijing
contact email	lileyuan2016@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/2025/08/PXD056968

PRIDE project URI

• PRIDE
  1. PXD056968
     1. Label: PRIDE project
     2. Name: Systematic Metaproteomic Mapping of Ex vivo Gut Microbiota Functional Responses to Therapeutic Drugs (3)