Microbiome-based study in wild-caught Scomber scombrus fish products at the end of the supply chain

Abstract

Fresh fish remain the dominant seafood forms and preservation technologies have enabled them to access ever more distant markets. In this study, we used metabarcoding of the 16S rRNA gene to generate gill microbiomes from Scomber scombrus bought at fishmonger's stores as fresh products but whose labels showed they had been harvested in the Atlantic or Mediterranean FAO fishing areas. Microbial data were analysed with the aim of evaluating their ability to maintain signals from their different geographical origins and the presence of taxa which can potentially act as spoilers, foodborne pathogens, or histamine producers. Results revealed that microbiota, at the end of the wild fish supply chain, had differences related to the two FAO fishing areas (Atlantic vs Mediterranean). Despite the presence of microbial genera potentially associated with spoilage, histamine-production or foodborne pathogens, their patterns confirmed that low-temperature storage is a traditional but effective method of preservation. However, the ongoing spoilage processes were more evident in fresh non-local specimens, dominated by psychrophilic Gram-negative bacteria, whereas fresh local specimens contained Planctomycetes taxa. Therefore, despite the current limitations mainly related to time and cost of the method, our study highlighted that microbiome-based applications are an emergent tool for food system transformation.