Microbial community shifts in oxygen-permeable vacuum skin packaged seafood during refrigerated storage
This BioProject contains raw high-throughput 16S rRNA gene amplicon sequencing data generated to characterize bacterial community dynamics and spoilage-associated succession in commercially produced, oxygen-permeable vacuum skin packaged (VSP) seafood during refrigerated storage. Vacuum skin packaging is designed to create a skin-tight, hygienic barrier that conforms to the product and tray, improves presentation, and reduces exposure to handling and environmental contamination. For fresh seafood, oxygen-permeable VSP films are used to maintain aerobic conditions while still providing the benefits of vacuum skin packaging, making VSP a practical alternative to traditional overwrap or tray/film systems for refrigerated retail display.The primary objective of this project is to evaluate the refrigerated shelf-life trajectory of multiple VSP seafood commodities and to describe how the bacterial community shifts across storage time under a single packaging format. Ten VSP seafood products were obtained from a seafood processor in Florida (USA): flounder, mahi, perch, salmon, scallop, shrimp, snapper, swai, tilapia, and tuna. Packaged products were thawed under refrigeration (4 C) and stored under refrigeration to mimic common U.S. retail handling and display conditions. Samples were evaluated at three timepoints (day 1, day 5, and day 9) representing early, mid, and late refrigerated storage. At each timepoint, conventional culture-based microbiological enumeration was performed to quantify aerobic plate counts, coliforms, and lactic acid bacteria, providing complementary indicators of microbial growth and spoilage progression and enabling comparison between culture-based indicators and community profiles.In parallel, total microbial DNA was extracted from seafood samples and used for bacterial community profiling by sequencing the V4 hypervariable region of the 16S rRNA gene. This BioProject/SRA submission includes the raw sequencing reads (FASTQ) and associated sample metadata describing seafood type, packaging condition (oxygen-permeable VSP), storage temperature, and storage timepoint. Sequence data were processed and analyzed using standard amplicon bioinformatics approaches (including quality filtering, read assignment, and taxonomic profiling) to evaluate changes in relative abundance, community diversity, and dominance patterns of key psychrotrophic and spoilage-associated taxa over time. Across products and storage timepoints, dominant genera observed in this study include Photobacterium, Psychrobacter, Pseudomonas, and Brochothrix, with Pseudomonas increasing in relative abundance by mid-storage in multiple products.Overall, this dataset provides a comparative, multi-commodity resource for understanding how bacterial communities shift during refrigerated storage of oxygen-permeable VSP seafood. The data support shelf-life assessment and evidence-based handling guidance that processors and retailers can use to manage display time, reduce spoilage-related losses, and protect consumers. The dataset can also be reused for cross-product comparisons, method development (including integration with qPCR or digital PCR quantification), and meta-analyses focused on spoilage ecology, psychrotrophic growth under refrigeration, and packaging effects on microbial succession in seafood.To facilitate reuse, sample identifiers and metadata enable stratification by seafood commodity and storage timepoint (day 1, 5, and 9 at 4 C). These data are intended for amplicon-based bacterial community analysis (not whole-genome metagenomics). No human subject data are included. The linked study relates community shifts to culture-based counts across storage, allowing future users to benchmark microbial succession against practical spoilage indicators and to compare oxygen-permeable VSP seafood with other packaging formats in meta-analyses.