基于高通量测序技术分析奶牛场垫沙和橡胶垫卧床中的菌群差异. (Chinese)

Analysis of microbial community difference between sand and rubber bedding in dairy farm by high throughput sequencing technology. (English)

In order to explore the characteristics and differences of the microbial flora of the sand bedding and rubber bedding of dairy farms, 6 samples of sand bedding and rubber bedding were collected from two dairy farms in Sichuan Province,and the sequencing and bioinformatics of 16S rRNA gene in V4 area was analyzed by high-throughput sequencing technology. The results showed that a total of 1 443 818 clean reads were obtained from the 12 samples of the bedding material of the two dairy farms. The effective sequences with a similarity of 97% were subjected to operational taxonomic units (OTUs), and a total 2 311 OTUs were produced. At the level of genus classification, the dominant bacteria in the sand bedding were Acinetobacter, Marinobacter, Riemerella, Corynebacterium, Arthrobacter. The dominant bacteria in the rubber bedding were Corynebacterium, Luteimonas, Fusobacterium,Halomonas, and Vibrio. The relative abundance of Acinetobacter and Riemerella in the sand bedding samples was significantly higher than that of the rubber bedding samples (P<0.05), but the relative abundance of Fusobacterium in the rubber bedding samples was significantly higher than that of the sand bedding sample (P<0.05). Chao index, Ace index, Shannon index and Simpson index were not significantly different between the two groups (P>0.05). The results indicated that difference of the microbial flora between sand bedding samples was greater than the rubber bedding samples, whether it was sand or rubber bedding, there were pathogenic bacteria in environmental conditions. [ABSTRACT FROM AUTHOR]

为探究奶牛场沙土垫层和橡胶垫层菌群特征及差异,分别采集四川省两个规模化奶牛场的沙土垫层样本和橡胶垫层样本各6份,利用高通量测序技术对16S rRNA基因的V4区进行测序和生物信息学分析。结果显示,两个奶牛场的卧床垫层12个样本共获得1 443 818条优化序列(clean reads),将相似度为97%的有效序列进行操作分类单元(operational taxonomic units,OTUs)聚类,共得到2 311个OTUs。在属分类水平上,沙土垫层优势菌属为不动杆菌属(Acinetobacter)、海杆菌属(Marinobacter)、里氏杆菌属(Riemerella)、棒状杆菌属(Corynebacterium)、节杆菌属(Arthrobacter);橡胶垫层优势菌属为棒状杆菌属(Corynebacterium)、藤黄单胞菌属(Luteimonas)、梭杆菌属(Fusobacterium)、盐单胞菌属(Halomonas)、弧菌属(Vibrio)。沙土垫层样本中不动杆菌属(Acinetobacter)、里氏杆菌属(Riemerella)的相对丰度显著高于橡胶垫层样本(P<0.05),橡胶垫层样本中梭杆菌属(Fusobacterium)的相对丰度显著高于沙土垫层样本(P<0.05)。Chao指数、Ace指数、Shannon指数、Simpson指数在两组之间差异均不显著(P>0.05)。结果表明,沙土样本间的菌群差异大于橡胶垫层样本,无论是沙土垫层还是橡胶垫层,均存在环境条件致病菌。 [ABSTRACT FROM AUTHOR]

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