PXD075819-1

PXD075819 is an original dataset announced via ProteomeXchange.

Title	Impact of size exclusion chromatography on the purity and proteomic profiles of extracellular vesicles derived from Lactobacillus reuteri
Description	Extracellular vesicles (EVs) produced by probiotic bacteria are increasingly recognized as key mediators of host-microbe communication. However, the molecular composition and biological interpretation of bacterial EV proteomes are strongly influenced by the isolation method used. Here, we systematically compared ultracentrifugation (UC) and size exclusion chromatography (SEC) for isolating EVs from Lactobacillus reuteri DSM 20016 and evaluated their effects on vesicle yield, purity, and proteomic profiles. Although UC generated a significantly higher EV yield than SEC, it resulted in substantially lower purity, as indicated by elevated protein contamination and a reduced particle-to-protein ratio. In contrast, SEC improved EV purity by approximately 6.45-fold, demonstrating more effective removal of non-vesicular proteins. Quantitative proteomics identified 982 proteins in bacteria, 677 in UC-EVs, and 861 in SEC-EVs. UC-EVs were predominantly enriched in cytosolic metabolic enzymes, ribosomal proteins, and macromolecular complex-associated components, consistent with co-sedimentation artifacts during high-speed UC. However, SEC-EVs showed selective enrichment of membrane-associated and cell wall-modifying proteins, including peptidoglycan hydrolases, lipoproteins, holin, lytic transglycosylase, penicillin-binding protein, and sulfatase, supporting their origin from regulated envelope remodeling processes. Notably, SEC-EVs contained several proteins including NLP/P60 protein, peptidoglycan hydrolases, EPS biosynthesis-related enzymes, and lipoproteins implicated in anti-inflammatory activities. Overall, our findings demonstrate that EV proteomes are highly isolation-dependent and identify SEC as a superior approach for enhancing proteomic specificity and biological interpretability in bacterial EV research.
HostingRepository	PRIDE
AnnounceDate	2026-09-01
AnnouncementXML	Submission_2026-08-31_21:22:07.937.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dongsic Choi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-18 19:22:27	ID requested
⏵ 1	2026-08-31 21:22:08	announced

10.1021/ACS.JPROTEOME.6C00305;

submitter keyword: membrane vesicles, exosomes, inflammation, lactic acid bacteria,Limosilactobacillus

Dongsic Choi
contact affiliation	Department of Biochemistry, Soonchunhyang University, College of Medicine, Cheonan, 31151, Republic of Korea
contact email	dongsic@sch.ac.kr
lab head
Dongsic Choi
contact affiliation	Department of Biochemistry, Soonchunhyang University, College of Medicine 31 Suncheonhyang 6-gil, Bongmyeong-dong, office# 310 Cheonan-si, Chungcheongnam-do, 31151
contact email	dongsic@sch.ac.kr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD075819
     1. Label: PRIDE project
     2. Name: Impact of size exclusion chromatography on the purity and proteomic profiles of extracellular vesicles derived from Lactobacillus reuteri