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 (<i>Allium cepa</i>) and cabbage (<i>Brassica oleracea</i>) microgreens cultivated on soil, biostrate, and jute fiber substrates, with and without <i>Salmonella</i> 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.