摘要
Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.
摘要译文
反刍动物生产的肉和牛奶是重要的农产品，是人类蛋白质的主要来源。反刍动物的生产具有相当大的经济价值，是世界许多地区粮食安全的基础。然而，由于自然资源减少和生产成本随之增加，以及农业反刍动物对环境影响的认识提高，该部门面临重大挑战。饲料的消化和肠道甲烷的产生是关键功能，可以通过彻底了解瘤胃微生物组来控制。 DNA测序技术和生物信息学的进步正在改变我们对复杂微生物生态系统的理解，包括哺乳动物的胃肠道。将这些技术应用于瘤胃生态系统已经允许在不同的饮食和生产条件下研究微生物多样性。此外，来自几种培养的瘤胃细菌和古细菌物种的基因组测序提供了关于其生理学的详细信息。最近，宏基因组学，主要旨在了解植物结构多糖降解所涉及的酶机制，开始通过允许进入整个群落并回避种植所施加的限制来产生新的见解。这些进展突出了这些方法对瘤胃微生物群落结构特征的预示，并将其与瘤胃微生物群的功能联系起来。使用高通量培养独立技术的初步结果也表明，瘤胃微生物组比人盲肠更复杂和多样化。因此，对其基因进行编目将需要相当多的测序和生物信息学努力。然而，通过宏基因组学和关键群体的基因组测序构建瘤胃微生物基因目录是可实现的目标。瘤胃微生物基因目录对于了解微生物组的功能及其与宿主动物和饲料的相互作用是必要的，它将为综合微生物组 - 宿主模型提供基础，并为促进污染较少，更强大和有效的反刍动物提供策略。
D. P. Morgavi (a1); W. J. Kelly (a2); P. H. Janssen (a2);G. T. Attwood (a2). Rumen microbial (meta)genomics and its application to ruminant production[J]. animal, 2013,7(Sup1): 184-201