Purpose: The objective of this study was to examine the microbiome of hot smoked salmon over a 5-week refrigerated shelf life using traditional microbiological and next-generation sequencing methodologies.
Methods: Hot smoked salmon fillets were stored aerobically at 4°C for 35 days with duplicate sampling on days 0, 4, 7, 10, 14, 17, 21, 27, and 35. Traditional culture-based methods were used to determine aerobic plate count and lactic acid bacteria count, and representative isolates were chosen for genotyping by RS-RAPD. Microbial diversity was characterized by deep sequencing of 16S rRNA gene amplicons using the Illumina MiSeq platform. Sequencing data were analyzed using QIIME 1.8.
Results: Microbiome analysis depicted a complex initial diversity that decreased from day 7 through 17 but rebounded at day 21. Photobacterium, Pseudomonas and Acinetobacter were initially predominant, followed by a transition towards a population dominated by Moraxcellaceae. Spoilage populations beyond 3 weeks include Staphylococcus and Micrococcaceae. Brochothrix were observed as major constituents throughout, except during an intermediate spoilage period. Total mesophilic APC reached 2.8 x 107 CFU/g after 5 weeks, from which isolates clustered into 8 major clades by genotyping. Total LABs steadily increased to 2.0 x 106 CFU/g and yeasts to 3.2 x 105 CFU/g over the same period. Enterococcal populations remained near detection limits until day 21, after which sporadic growth to 1.0 x 105 CFU/g was observed. Genotyping of 198 isolates revealed temporal relationships complementary to deep sequencing data.
Significance: Traditional microbiological culture and next-generation sequencing yielded complementary data that deepen understanding of microbial population dynamics during refrigerated storage of smoked salmon, and may enable targeted and more effective methods to increase shelf life.