High-throughput DNA sequencing with the Illumina MiSeq platform was used to analyze the microbial communities in hairtail (Trichiurus haumela) muscle samples to study the diversity and dynamic changes in these communities during cold-chain circulation of these fish. The richness and diversity of the microbial community in hairtail muscle had a transient decline from 0 to 24 h and decreased after the first rise from 24 to 216 h. The diversity and richness of bacteria in cold-chain hairtail reached maximum at 168 h. The Shannon and Simpson diversity indices of the bacteria were 2.96 and 0.16, respectively, and their ACE and Chao1 richness indices were 254.84 and 155.10, respectively. The dominant bacteria belonged to phylum Proteobacteria, class Gammaproteobacteria, order Pseudomonadales, family Pseudomonadaceae, and genus Pseudomonas, and their relative abundances were 80.52, 72.11, 76.68, 23.25, and 53.50%, respectively. These results provide a basis for exploring how to maintain the freshness and predict the shelf life of hairtail.

  • Microbial communities in hairtail were analyzed with high-throughput DNA sequencing.

  • The richness and diversity of the microflora in hairtail were the lowest at 216 h.

  • The dominant bacteria in cold-chain hairtail at 216 h were Pseudomonas.

  • Inhibiting the growth of Pseudomonas might extend the shelf life of hairtail.

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