PXD066732-1

PXD066732 is an original dataset announced via ProteomeXchange.

Title	Metaproteomic analysis of non-IBD, UC and pouchitis patients stool samples berfore and on antibiotics treatment
Description	Antibiotics (Abx) are critical in modern medicine but can induce intestinal dysbiosis, exacerbate inflammatory bowel diseases (IBD), and disrupt the gut microbiome. Moreover, Abx treatment was reported as a significant risk factor for developing IBD, yet the underlying mechanisms remain unknown. Here, we employed metagenomics and metaproteomics to investigate the impact of Abx treatment on gut microbiota composition and activity in non-IBD, pouchitis, and ulcerative colitis (UC) patients. The combined analysis revealed distinct microbiome profiles for each group and found that the metaproteomes are more susceptible to Abx-induced changes than metagenomes. Alpha diversity decreased across all cohorts during Abx treatment, with pouchitis and UC patients exhibiting dysbiosis before treatment. Taxonomic shifts, including blooms of Proteobacteria and Actinobacteria, and reductions in microbial pathway abundances were more pronounced in IBD patients. Proteomic analysis revealed an elevated abundance of host pancreatic proteases, particularly in non-IBD patients, and during Antibiotic treatment, correlating with increased proteolytic activity and impaired gut barrier function. Functional assays confirm differential fecal proteolytic activity, suggesting that bacterial protease inhibitors, which are significantly depleted during Abx treatment, regulate proteolysis and thereby maintain delicate homeostasis in the gut. Overall, our findings suggest that Abx treatment disrupts the balance between bacterial protease inhibitors and host proteases, contributing to inflammation and gut barrier disruption. This work underscores the importance of understanding Abx-induced proteolytic shifts in the context of IBD and highlights the utility of metaproteomics in elucidating host-microbiome interactions. Future research should investigate the molecular mechanisms underlying the abundance and activity of bacterial protease inhibitors, as well as their impact on gut health.
HostingRepository	PRIDE
AnnounceDate	2026-04-30
AnnouncementXML	Submission_2026-04-29_16:17:38.625.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lior Lobel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-29 13:57:42	ID requested
⏵ 1	2026-04-29 16:17:39	announced

Dataset with its publication pending

submitter keyword: antibiotics,metaproteomics, IBD

Lior Lobel
contact affiliation	Faculty of Life Sciences,Bar-Ilan University, Israel
contact email	lior.lobel@biu.ac.il
lab head
Lior Lobel
contact affiliation	Bar-Ilan University
contact email	lior.lobel@biu.ac.il
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD066732
     1. Label: PRIDE project
     2. Name: Metaproteomic analysis of non-IBD, UC and pouchitis patients stool samples berfore and on antibiotics treatment