PXD058570

PXD058570 is an original dataset announced via ProteomeXchange.

Title	Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD
Description	Host-microbiome-dietary interactions play crucial roles in regulating human health, yet direct functional assessment of their interplays, cross-regulations and downstream disease impacts remains challenging. We adopted metagenome-informed metaproteomics (MIM), in both mice and humans, to simultaneously explore host, dietary, and species-level microbiome interactions across diverse scenarios, including commensal and pathogen colonization, nutritional modifications, and antibiotic-induced perturbations. Implementation of MIM in murine auto-inflammation and in human IBD characterized a ‘compositional dysbiosis’ and a concomitant, species-specific ‘functional dysbiosis’ driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutrient assessment enabled determination of IBD-related consumption patterns, dietary treatment compliance and small-intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology, while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.
HostingRepository	PRIDE
AnnounceDate	2025-06-10
AnnouncementXML	Submission_2025-06-10_07:51:04.506.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rafael Valdes-Mas
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: gut metagenome; NCBI TaxID: 749906; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-04 07:02:51	ID requested
⏵ 1	2025-06-10 07:51:04	announced

10.1016/J.CELL.2024.12.016;

submitter keyword: microbiome, diet, metagenomics-informed metaproteomics,Proteomics, host, biomarker

Eran Elinav
contact affiliation	Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
contact email	eran.elinav@weizmann.ac.il
lab head
Rafael Valdes-Mas
contact affiliation	Weizmann Institute Of Science
contact email	rvaldesmas@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/2025/06/PXD058570

PRIDE project URI

• PRIDE
  1. PXD058570
     1. Label: PRIDE project
     2. Name: Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD