Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits

Food-associated microorganisms represent a diverse reservoir of bacterial strains with functional traits potentially relevant to host–microbiome interactions, stress resilience, metabolic processes, and microbial competition. In this study, we performed a multi-omics characterization of food-origin bacterial isolates to identify a potential candidate strain for further studies on microbiome–microgreens interactions. Over one hundred bacterial isolates were initially recovered from various food products and subjected to molecular screening, followed by whole-genome sequencing, metabolic profiling, transcriptomic chcracterisation and morphological analysis of selected strains. Comparative characterization revealed significant differences among the strains. Among the tested isolates, strain B107/23, identified as Priestia megaterium (formerly Bacillus megaterium), had the highest number of genes associated with stress responses, nutrient uptake, plant growth-promoting traits, and colonization mechanisms. Phenotypic characterization later demonstrated high metabolic flexibility and a low substrate stress index, while transcriptomic profiling revealed the expression of genes associated with stress responses and metabolic activity. Overall, the integration of genomic, phenotypic, and transcriptomic results distinguished B107/23 as the most promising candidate among the tested isolates and revealed the molecular traits potentially significant to interactions between the microbe and the host. These findings provide a basis for the validation of the selected strain in microgreens systems, including studies addressing plant stress resilience and post-harvest quality.