Microbial profiling of oysters from a processing plant and retail products: Analysis based on culture-dependent methods and 16S rRNA gene sequencing

Oysters (Crassostrea gigas) are one of the most consumed shellfish globally. However, there is a lack of comprehensive microbiome studies that include the processing and distribution stages of oysters. The present study used both culture-based methods and 16S rRNA sequencing to produce comprehensive microbial profiles of oysters in two parts: (1) an oyster processing plant that processes raw and frozen oysters (n = 57) and (2) retail oyster products across two seasons (winter and spring) (n = 112). In the processing plant, shucking increased the aerobic plate count (APC) from 1.86 log CFU/g in freshly harvested oysters to 3.95 log CFU/g in shucked oysters. Controlling the washing process is important, as the APCs decreased after washing and remained level until the final products, raw and frozen oysters (2.54 and 2.34 log CFU/g, respectively). After desalting in the frozen oyster plant, the bacterial community shifted to be dominated by the family Spirochaetaceae, Mycoplasma, and Shigella taxa, indicating a need to control problematic bacteria in the desalting process. SourceTracker analysis revealed that raw materials contributed more to the microbiota of final products than environmental samples. In retail oyster products, APCs were marginally higher in spring (3.58 log CFU/g) than in winter (3.05 log CFU/g) samples. While bacterial count differences were not dramatic, the proportions of taxa in the microbial community differed by season. In winter retail products, Photobacterium (27.91 %) and Aliivibrio (20.42 %) dominated, while spring samples showed a diverse distribution of the family Vibrionaceae (19.90 %), Photobacterium (14.20 %), Psychromonas (11.84 %), and Aliivibrio (7.20 %). These findings contributed to our understanding of oyster microorganisms and identified food safety control points and cross-contamination sources. This in-depth understanding is expected to inform the development of fishery and seafood safety management measures.