PXD063844

PXD063844 is an original dataset announced via ProteomeXchange.

Title	Comparing and optimizing protein extraction methods for the analyses of human fecal microbiome via metaproteomics approach
Description	Metaproteomic analysis offers critical insights into gut microbiome function; however, efficient microbial protein extraction from fecal samples remains challenging due to the complexity of different types of bacterial cell walls in the microbiome. In this study, we systematically compared three representative detergent-based lysis buffers (SDS_urea, DDM_urea, SDS_DDM_urea) for metaproteomics sample preparation. After multiple levels of analyses, we identified SDS_DDM_urea as the most efficient option for extracting diverse microbial proteins, peptides, and identifying microbial species. Applying this optimized method to samples from a dietary intervention study (Summer Harvest Adventure), we found minimal group-level microbial diversity shifts during this type of intervention, but substantial individual-specific variations reflected by metaproteomics results. Functional analyses also revealed microbial protein changes, especially proteins related to metabolic adaptations, including enhanced carbohydrate metabolism, amino acid biosynthesis, vitamin transport, and increased expression of membrane-associated proteins. Our results highlighted the personalized microbiome response to dietary interventions and underscored the importance of selecting appropriate protein extraction methods to accurately capture microbiome functional dynamics in microbiome analyses via metaproteomics.
HostingRepository	iProX
AnnounceDate	2025-05-10
AnnouncementXML	Submission_2025-05-11_20:30:45.191.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gordon Zhang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	acetylated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-11 20:30:30	ID requested
⏵ 1	2025-05-11 20:30:45	announced

Dataset with its publication pending

submitter keyword: Metaproteomics, Gut microbiota, Protein extraction, Dietary intervention, Microbial diversity, Mass spectrometry, Microbial functional analysis

Chris Zhu
contact affiliation	Ohio State University
contact email	gao.2116@osu.edu
lab head
Gordon Zhang
contact affiliation	Ohio State University
contact email	nzhangwe@outlook.com
dataset submitter

iProX dataset URI