General information on the shotgun metagenomics sequence data acquired from an integrated crop-livestock system

The shotgun metagenomic dataset generated from goat manure and maize rhizosphere samples comprises 27 libraries with approximately 8–12 Gbp of high-quality sequences per sample after quality control. The datasets exhibit GC contents typical of soil and manure microbial communities (~60–66%). Sequence reads showed high base-calling accuracy with average Q30 scores exceeding 90%, indicating high sequencing quality across all samples. These data provide a comprehensive metagenomic resource for investigating microbial community composition and functional potential in integrated crop–livestock systems.