Metagenomic sequencing dataset of microbial communities in onion and cabbage microgreens across substrates, Salmonella inoculation, and bacteriophage application

This dataset comprises shotgun metagenomic sequencing results from edible portion of onion (Allium cepa) and cabbage (Brassica oleracea) microgreens cultivated on soil, biostrate, and jute fiber substrates, with and without Salmonella inoculation and bacteriophage application. Table 1 contains detailed sequencing quality metrics and National Center for Biotechnology Information Sequence Read Archive accession numbers (BioProject: PRJNA1327464) for all 24 samples. Figure 1 provides a species-level (≥5% relative abundance) heatmap highlighting microbial community clustering by seed type. These data can be reused for comparative microbiome analyses, evaluation of pathogen-phage-substrate interactions, and benchmarking of metagenomic workflows.