Purpose: The goals of this study were to analyze the microbial succession of raw salmon in a refrigerated shelf life model, identify potential spoilage microorganisms, and compare next generation sequencing with traditional microbiological methods.
Methods: Raw salmon fillets were stored aerobically at 4°C for a total of 14 days with duplicate sampling on days 0, 2, 4, 7 and 14. Aerobic plate count and lactic acid bacteria count were determined and representative isolates were genotyped by RS-RAPD. Microbial diversity was characterized by deep sequencing of 16S rRNA gene amplicons using the Illumina MiSeq platform and a QIIME 1.8 analysis pipeline.
Results: Aerobic plate counts were 6.03×105 CFU/g at day 0, increased rapidly to 3.24×108 CFU/g by day 4 before plateauing around 1.0×109 CFU/g. Lactic acid bacteria counts were 6.92×103 CFU/g at day 0, increased to 1.05×107 CFU/g by day 4, and slowly increased to 3.29×108 CFU/g by day 14. Genotypes from representative APC and LAB isolates clustered into 5 and 3 predominant clades, respectively. Based on number of unique sequences and Shannon diversity indices, samples at day 0 and 2 were least diverse with community complexity increasing over time. Deep sequencing indicated that proportions of taxa belonging to Listeraceae started to increase at day 4 with Carnobacteriaceae and Flavobacteriaceae becoming more predominant at day 7 and Enterococcaceae increasing at day 10. Vibrionaceae, Pseudomonadaceae and Moraxellaceae decreased in proportion of the total bacterial population over time, while increasing in abundance.
Significance: Next generation sequencing data corroborated traditional microbiological findings implicating lactic acid bacteria, specifically Carnobacteriaceae and Enterococcaceae as major spoilage microorganisms of raw salmon.