The gut microbiome of pigs is a complex microbial ecosystem critical to host health and agricultural productivity. While amplicon sequencing studies have expanded our understanding of this community, a lack of standardized data and metadata often hinders comparative analysis and data reuse. To address this challenge, we present the Pig Gut Microbiome Dataset (PGMD, version 1.0), a comprehensive resource developed through the systematic selection of publications, extensive manual curation of associated metadata, and standardized reprocessing of raw amplicon sequencing data. This initial release integrates 202 publications (encompassing 207 16S rRNA gene sequencing data BioProjects), comprising 12,336 samples, collected from 22 countries. The dataset encompasses 52 host species and 3,028 taxonomic groups. Samples are systematically categorized by research topics and host phenotypes, enabling users to explore microbial community composition, identify differentially abundant taxa across experimental conditions and phenotypes, investigate six core phenotype-associated microbial clades, and determine dominant taxa across four key growth stages. PGMD significantly enhances the standardization and integration of pig gut microbiome data, serving as a valuable resource for research towards precision feeding and improved animal health. All data in the dataset are hosted and available in figshare https://doi.org/10.6084/m9.figshare.25911745.v1.
Geng et al. (Mon,) studied this question.