Integrative culture-based and 16S rRNA microbiome analysis combined with on-site temperature evaluation to enhance safety management of salt-fermented octopus and clams

Abstract

Salt-fermented octopus and clams are representative ready-to-eat raw seafood side-dishes consumed year-round across various distribution channels. Since high salinity and fermentation are perceived as safe, there is often insufficient attention paid to microbial control. This study assessed the microbial quality of commercial products by analyzing temperature profiles, contamination levels, and microbiome dynamics. Seasonal and distributional factors were considered as key environmental variables to examine their impact on microbial quality heterogeneity. A total of 115 salt-fermented seafood samples were collected from three distribution channels (local market, market, online) across four seasons. Variations in temperature and microbial contamination, including aerobic plate counts (APC), coliforms, and foodborne pathogens such as Escherichia coli, were identified across samples. Microbial diversity was analyzed via 16S rRNA gene sequencing. Numerous samples exceeded recommended temperature thresholds, particularly during the summer season, indicating frequent temperature abuse that directly influenced microbial community composition and diversity. Temperature abuse revealed a gap between food safety policy and on-site practices. APC ranged 3–4 log CFU/g, and coliform counts were detected in fall samples from local markets. In the case of the qualitative analysis, only E. coli was detected from local market samples in fall. Microbiome analysis revealed distinct seasonal and channel-specific shifts, with Leuconostocaceae dominant in octopus and Moraxellaceae and Halomonadaceae in clams, reflecting differing fermentation and environmental adaptations. The findings of this study regarding the distinct microbial profiles according to season and distribution channels provide practical guidance for developing risk management strategies optimized for the determinant factors of microbial heterogeneity. © 2025 Elsevier Ltd