NEXT GENERATION MICROBIOLOGICAL RISK ASSESSMENT: NEXT GENERATION SEQUENCING (NGS) FOR THE DETERMINATION OF FISH FLESH MICROBIOTA

摘要

The objective of the study is the assessment of the microbial ecology and safety of fisheries in Greece using next-generation sequencing (NGS). 14 fish samples were obtained from local fish stores (Greece) within 1 day from capture. The initial microbiota in fish flesh was determined using next-generation sequencing (NGS). The main pathogenic bacterial species identified in the tested fish samples included Vibrio spp., Clostridium spp., Staphylococcus, Flavobacterium and Janthinobacterium representing both native freshwater habitats and contaminants arising from different sources, including sewage and direct contamination by wild animals, livestock, and feed. The initial spoilage microbiota of fish consisted of various psychrotrophic Gram-negative bacteria, mainly Pseudomonas, Acinetobacter, Moraxella, Shewanella, Psychrobacter, Lactobacillus, Brochothrix and Photobacterium. The results of the study indicate the applicability and usefulness of NGS for the determination of microbial flora associated with food-borne diseases and spoilage in fish products.