Microbiome profiling in fresh-cut products

Fresh-cut fruits and vegetables are highly perishable and minimally processed products. One of the main issues related to their safety is the potential microbial contamination and spoilage that can significantly reduce their shelf-life. To tackle this problem, the complete identification of fresh-cut product microbiota is of primary importance. Indeed, despite the huge amount of metagenomics data generated in the last decade to profile food microbiome, a specific knowledge about fresh fruits and vegetables microbiome is still scarce. Production of additional food-related data, such as improved microbial genome assemblies and increased number of microbial reference genome sequences, are needed to perform a robust and reliable analysis of food-related metagenomics data. These data can be successfully applied to model the contribution of individual microorganisms for the quality and safety of fresh-cut products.