Evaluation of the Bacterial Diversity in Cured Fish Samples Collected from Enshi by PCR-DGGE and MiSeq High-throughput Sequencing
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Abstract:
Cured fish is a kind of Chinese traditional food which is popular for its unique taste and flavor.The bacterial diversity of cured fish samples collected from Enshi was studied by 16s rDNA gene-based PCR-DGGE and MiSeq high-throughput sequencing. The result of PCR-DGGE indicated that the domain bacteria in cured fish samples were belong to Psychrobacter and Lactobacillus. The result of MiSeq high-throughput sequencing indicated that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria constituted more than 1.0% of total sequences at the phylum level, with the relative abundance of 61.29%, 30.21%, 5.34%, and1.74%, respectively. Meanwhile, Psychrobacter, Brochothrix, Pseudomonas, Staphylococcus, Acinetobacter, Vibrio, Pseudoalteromonas, and Chryseobacterium constituted more than 1.0% of total sequences at the genus level, with the relative abundance of 35.70%, 19.74%, 7.13%, 7.12%, 4.19%, 3.90%, 3.09%, and 1.98%, respectively. At the OTU level, 64 OTUs were found with the cumulative average relative was 62.67% of total qualified sequences. Thus, the main dominant bacteria in cured fish samples were composed of Psychrobacter belonging to Proteobacteria and Brochothrix belonging to Firmicutes, and all samples shared a large number of core bacterial microbiome.
