Decoding stress responses in the pig gut microbiome: a metaproteomic perspective for biomarker discovery

This repository contains the metagenome-assembled genomes (MAGs) reconstructed from faecal shotgun metagenomic sequencing of 60 pigs subjected to chronic social stress (reduced space allowance) or control conditions.These MAGs were generated as part of a genome-resolved metaproteomic study investigating the functional response of the pig gut microbiome to chronic social stress. The MAGs served as the custom protein sequence database for nano LC-MS/MS-based metaproteomic searches, enabling the direct linkage of expressed proteins to their source microorganisms. This integrated metagenomics–metaproteomics approach allowed the quantification of metabolically active microbial populations and the identification of stress-responsive taxa and functions through Partial Least Squares Discriminant Analysis (PLS-DA), achieving a group discrimination accuracy of 99.51%. Briefly, total DNA was extracted from faecal samples and sequenced on the Illumina NovaSeq 6000 platform (~18 Gb per sample, 2 × 150 bp paired-end reads). Reads were quality-filtered and host-decontaminated using the nf-core/mag 3.3.0 pipeline. Assembly was performed with Megahit v1.0.2 (individual and co-assemblies per pen). Binning was carried out with SemiBin2 and MetaBAT2, bins were refined with DAS Tool, and dereplicated with dRep v3.5.0 (minimum completeness 70%, maximum contamination 10%). Quality assessment was performed with CheckM2, and taxonomic annotation with GTDB-Tk v2.4.1. The final catalogue contains 483 MAGs (478 bacterial, spanning 408 species, and 5 archaeal), of which 257 (49.13%) are high quality genomes (completeness >90%, contamination <5%) following MIMAG standards.