Metagenome and Metatranscriptome Analysis of Sprout Spent Irrigation Water Microbiome Due to Salmonella Contamination of Alfalfa Seeds

Sprouts have been associated with numerous outbreaks caused by various pathogens including Salmonella and Escherichia. coli O157: H7. Sprout spent irrigation water (SSIW), i.e., the water that has flowed through the sprouts during production, can provide a representative sample of the entire microbial population, including pathogens, in the batch of sprouts. The purpose of this study is to examine the dynamics and functional activity of bacterial community in spent irrigation water during sprouting of Salmonella contaminated alfalfa seeds by shotgun metagenomics and metatranscriptomics.