Tennant Richard K, Sambles Christine M, Diffey Georgina E, Moore Karen A, Love John
Biosciences, University of Exeter.
Biosciences, University of Exeter;
J Vis Exp. 2017 Jan 13(119):54936. doi: 10.3791/54936.
Metagenomics is defined as the direct analysis of deoxyribonucleic acid (DNA) purified from environmental samples and enables taxonomic identification of the microbial communities present within them. Two main metagenomic approaches exist; sequencing the 16S rRNA gene coding region, which exhibits sufficient variation between taxa for identification, and shotgun sequencing, in which genomes of the organisms that are present in the sample are analyzed and ascribed to "operational taxonomic units"; species, genera or families depending on the extent of sequencing coverage. In this study, shotgun sequencing was used to analyze the microbial community present in cattle silage and, coupled with a range of bioinformatics tools to quality check and filter the DNA sequence reads, perform taxonomic classification of the microbial populations present within the sampled silage, and achieve functional annotation of the sequences. These methods were employed to identify potentially harmful bacteria that existed within the silage, an indication of silage spoilage. If spoiled silage is not remediated, then upon ingestion it could be potentially fatal to the livestock.
宏基因组学的定义是对从环境样本中纯化的脱氧核糖核酸（DNA）进行直接分析，并能够对其中存在的微生物群落进行分类鉴定。存在两种主要的宏基因组学方法；对16S rRNA基因编码区域进行测序，该区域在不同分类群之间表现出足够的差异以进行鉴定，以及鸟枪法测序，其中分析样本中存在的生物体的基因组并将其归为“操作分类单元”；根据测序覆盖范围的程度分为种、属或科。在本研究中，使用鸟枪法测序来分析牛青贮饲料中存在的微生物群落，并结合一系列生物信息学工具对DNA序列读数进行质量检查和过滤，对采样青贮饲料中存在的微生物种群进行分类，以及对序列进行功能注释。这些方法被用于识别青贮饲料中存在的潜在有害细菌，这是青贮饲料变质的一个迹象。如果变质的青贮饲料得不到补救，那么家畜摄入后可能会致命。
