PXD063155-1

PXD063155 is an original dataset announced via ProteomeXchange.

Title	Pig Feces Metaproteome, LC-MSMS, TMT12Plex
Description	Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a TMT LC-MSMS metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and four weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.
HostingRepository	PRIDE
AnnounceDate	2025-05-26
AnnouncementXML	Submission_2025-05-25_16:15:25.937.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD063155
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cary Davies
SpeciesList	scientific name: Fungi; NCBI TaxID: NCBITaxon:4751; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	amidated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-21 09:22:36	ID requested
⏵ 1	2025-05-25 16:15:26	announced

Rivera I, Harlow K, Cole RN, O'Meally R, Garrett W, Xiong W, Oliver W, Wells JE, Summers KL, Chhetri N, Postnikova O, Rempel L, Crouse M, Neville B, Davies CP, A metaproteomic analysis of the piglet fecal microbiome across the weaning transition. Front Microbiol, 16():1504433(2025) [pubmed]

10.6019/PXD063155;

10.3389/fmicb.2025.1504433;

submitter keyword: LC-MSMS, metaproteome, TMT,pig

Cary Pirone Davies
contact affiliation	United States Dept Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory
contact email	cary.davies@usda.gov
lab head
Cary Davies
contact affiliation	United States Department of Agriculture
contact email	cary.davies@usda.gov
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/2025/05/PXD063155

PRIDE project URI

• PRIDE
  1. PXD063155
     1. Label: PRIDE project
     2. Name: Pig Feces Metaproteome, LC-MSMS, TMT12Plex