Microbial succession and spoilage dynamics revealed by multi-omics in Norway lobster (Nephrops norvegicus) during ice storage

Abstract

The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.