Microbial Community Dynamics and Salmonella Persistence in Microgreen Cultivation: Impact of Growing Substrates and Phage Biocontrol

Microgreens are immature vegetable greens harvested after the development of cotyledonary leaves, representing an emerging category of produce that has gained significant popularity in recent years. Despite their nutritional and functional benefits, microgreens have been associated with recalls in the United States and Canada due to contamination with pathogens such as Salmonella and Listeria monocytogenes, raising important food safety concerns.Although research on microgreen cultivation is expanding, a critical knowledge gap remains regarding the combined effects of growing substrates and phage biocontrol on microbial communities and pathogen persistence. To address this, the objectives of this study are to: (1) examine microbial community dynamics and the persistence of Salmonella in different growing substrates during microgreen cultivation, and (2) investigate the influence of phage biocontrol on both microbial community dynamics and the survival of Salmonella during microgreen cultivation.In this study, Salmonella inoculum was introduced during the sowing of cabbage and onion microgreens, which were cultivated on three different substrates (soil-based, jute fiber, and Biostrate mat). A commercially available Salmonella-specific bacteriophage was applied by spraying either immediately after the blackout period or 24 hours before harvest. Following harvest, DNA was extracted from the edible portions of the microgreens and subjected to shotgun metagenomic sequencing.