基于高通量测序分析不同品种水牛生乳中细菌多样性

目的 利用16S rRNA高通量测序研究广西水牛研究所种畜厂内摩拉、尼里-拉菲及三品杂3品种水牛生鲜乳中的细菌多样。方法 提取当天采集的生水牛乳样本细菌总DNA,PCR扩增细菌的16S rDNA,纯化PCR扩增目的片断,将PCR产物与pMD18-T载体连接,构建其菌群的16S rDNA文库。用Miseq对其16S rRNA基因的V3-V4可变区进行测序以及BLAST比对。结果 3品种27个样本共获得1223个OUTs, M、N、S独有的OTU分别为295、41和42,共有OTU为511。物种组成与丰度差异显示：3品种优势菌门为：变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)。优势菌属为：金黄杆菌属(Chryseobacterium)、不动杆菌属(Acinetobacter)、乳球菌属(Lactococcus)、假单胞菌属(Pseusomonas)。样本层级聚类显示：3品种样本间菌落组成相似度较高。PCA与PLS-DA分析表明：3品种样本组内菌群多样性差异不显著,但组间菌群丰度差异明显。结论 摩拉、尼里-拉菲及三品杂水牛生鲜乳中细菌菌群均呈现较丰富的多样性,其共有的优势菌群为金黄杆菌(Chryseobacterium)、不动杆菌(Acinetobacter)、乳球菌(Lactococcus)、假单胞菌(Pseusomonas)。各品种间菌群组成种类整体相似,但其主要菌落丰富度差异明显。

Bacterial diversity of fresh milk in different buffalo breeds by high throughput sequencing

objective This study was to investigate the bacterial diversity of fresh milk in Murruh buffaloes, Nili-Ravi buffaloes and their crossbred with Chinese local buffaloes. Methods Fresh milk samples were taken from water buffaloes for total bacterial DNA extraction. V3-V4 variable regions of 16S rDNA were amplified and purified and then the amplicons were conjuncted with PMD-18 vecoter for the construction of 16S rDNA library and sequencing. Results The results shown that 1223 OTUs were obtained from 27 samples in three water buffalo breeds. The unique OTU numbers of fresh milk were 295,41,42 in Murruh buffaloes, Nili-Ravi buffaloes and their crossbred with Chinese local buffaloes, respectively. The shared OTU numbers was 511. For all breeds milk samples, the dominant phylums were Proteobacteria,Firmicutes and Bacteroidetes,the dominant genus were Chryseobacterium, Acinetobacter, Lactococcus and Pseusomonas. The sample level clustering results showed that the similarity of bacterial composition among the three breeds was very high. However, the PCA and PLS-DA analysis results showed that buffaloes breeds have no significant diferences on milk bacterial diversity even the abundance were different. Conclusion It can be concluded that the bacterial diversity of fresh milk in three buffalo breeds are very high and the dominant bacteria were Chryseobacterium, Acinetobacter,Lactococcus, Pseusomonas. The composition of the bacterial was similar among the varieties, but the abundance of the main bacterial was obviously different.