基于PCR-DGGE与高通量测序技术的恩施地区腊鱼细菌多样性评价

作为我国传统的发酵食品,腊鱼因具有独特的滋味和口感而深受人们青睐。以16 s rDNA基因为标靶,采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)与Mi Seq高通量测序技术相结合的方法对采集自恩施地区腊鱼样品的细菌多样性进行了研究。PCR-DGGE结果表明,腊鱼样品中的细菌以Psychrobacter和Lactobacillus为主。Mi Seq高通量测序结果表明,腊鱼中的优势细菌门主要为变形菌门(Proteobacteria)、硬壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria),其平均相对含量分别为61.29%、30.21%、5.34%和1.74%。腊鱼中的优势细菌主要为Psychrobacter、Brochothrix、Pseudomonas、Staphylococcus、Acinetobacter、Vibrio、Pseudoalteromonas和Chryseobacterium,其平均相对含量为35.70%、19.74%、7.13%、7.12%、4.19%、3.90%、3.09%和1.98%。在分类操作单元(Operational taxonomic units,OTU)水平上,发现了64个核心OTU,累计平均相对含量高达62.67%。由此可见,恩施地区腊鱼中的优势细菌主要由隶属于Proteobacteria的Psychrobacter及隶属于Firmicutes的Brochothrix构成,且不同样品共有大量的核心细菌菌群。

Evaluation of the Bacterial Diversity in Cured Fish Samples Collected from Enshi by PCR-DGGE and MiSeq High-throughput Sequencing

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.