To investigate the bacterial community diversity and functional differences in Litopenaeus vannamei during mid- and late-storage at room temperature and under refrigeration.

The bacterial community structure of Litopenaeus vannamei during mid- and late-storage at room temperature and under refrigeration (4 °C) was characterized by 16S rDNA sequencing. The Kyoto encyclopedia of genes and genomes(KEGG) database was used to predict the functional differences of spoilage bacteria in Litopenaeus vannamei stored at room temperature and under refrigeration during different storage periods.

Phylum-level analysis revealed Firmicutes as the predominant lineage (>95.5%) in spoiled Litopenaeus vannamei. At the genus level, mid-stage room temperature storage was characterized by the co-dominance of Family_XI_unclassified (32.59%), Tissierella (19.97%),Vagococcus (8.00%) and Kurthia (6.00%). This assemblage transitioned to a Peptostreptococcus (26.60%),Family_XI_unclassified (26.56%), Vagococcus (12.90%), Tissierella (5.95%) consortium at late-stage room temperature storage. Conversely, refrigeration significantly attenuated the relative abundance of spoilage-associated Kurthia and Peptostreptococcus, while concomitantly enriching Vagococcus (16.03%→22.86%), Peptoniphilu (9.24%→17.34%),Family_XI_unclassified (<0.5%→12.04%) and Tissierella (0.06%→10.11%) at terminal storage. KEGG-based functional prediction revealed that mid-stage bacterial communities under room-temperature storage upregulated nutrient acquisition, energy metabolism, and nucleotide biosynthesis pathways, conferring competitive growth advantages. Compared with room temperature storage, the abundance of certain nucleotide biosynthesis pathways was downregulated during mid-refrigerated storage, which contributed to the suppression of spoilage bacterial growth. At the end of storage, bacteria coped with adverse conditions by upregulating genetic material synthesis to repair temperature-induced DNA damage, and enhancing amino acid metabolism and cell wall reinforcement pathways to improve survival and adaptability.

The dominant spoilage bacteria in Litopenaeus vannamei stored at room temperature and under refrigeration partially overlap, yet their relative abundances differ significantly.Refrigeration exerts a certain inhibitory effect on spoilage bacteria of Litopenaeus vannamei, altering the community structure of dominant spoilage bacteria, and consequently resulting in functional differences.