SESPig gut microbiome strain-level genome catalog

Dietary fiber is a major energy source for pigs through microbial fermentation, and the capacity for fiber utilization depends in part on the repertoire of carbohydrate-active enzymes (CAZymes) encoded by the gut microbiome. However, genome-resolved references for indigenous pig breeds remain limited, and catalogs based solely on short-read metagenomics often produce fragmented assemblies that constrain taxonomic resolution and functional inference. To facilitate genome-based studies of fiber degradation in pigs, we generated a strain-level genome catalog for the Small-ear spotted pig (SESPig) by integrating Illumina short-read metagenomics, Oxford Nanopore Technologies (ONT) long-read metagenomics, and cultivation-based genomics.This dataset contains 975 non-redundant genomes, including 942 metagenome-assembled genomes (MAGs) reconstructed from 11 Illumina metagenomes and one pooled ONT metagenome, as well as 33 isolate genomes obtained from cultured strains. Genome quality metrics (completeness and contamination), assembly statistics (e.g., genome size and N50), and taxonomic assignments were generated using a standardized genome-resolved workflow. Across the catalog, genomes span 15 phyla and 87 families, dominated by Bacillota and Bacteroidota. Using GTDB-Tk classification, 754 genomes were assigned to existing GTDB species, whereas 221 genomes lacked species-level assignments and may represent putative novel species.