Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria

联合国粮食及农业组织预测，由于收入增加和世界人口增长，到2050年全球肉类和牛奶需求将分别增长76%和63%。这将需要改进可持续的畜牧生产系统。牛的大前肠，即瘤胃，每克食糜（食物消化时的物质）含有数十亿微生物（微生物组）。这些微生物将人类不可食用的食物（如草）发酵成营养物质，宿主动物将其转化为高质量的产品，如肉和奶。这种瘤胃微生物生态系统对动物来说是必不可少的，但对环境有一个缺点，因为一些微生物会产生强效的温室气体甲烷。该项目将利用瘤胃微生物信息作为动物育种标准，以提高饲料转化率，同时减少甲烷排放，从而解决这些挑战。在这项研究中，我们将估计动物基因组与其瘤胃微生物组之间的联系程度，并利用大量繁殖种群调查其联系的原因。该种群由我们的商业合作伙伴Genus plc提供，结构良好，可确保准确估计宿主对微生物组的遗传影响。我们前期的研究表明，瘤胃微生物基因丰度与饲料转化率和甲烷排放密切相关。然而，宿主动物基因组如何以及在多大程度上影响微生物基因的丰度尚不清楚，将在本项目中进行研究。由于这些微生物基因的代谢功能大多是已知的，我们期望在宿主动物和特定瘤胃微生物功能之间发现许多新的遗传联系，这些联系甚至可能在物种之间保守。与动物基因组相关的瘤胃微生物基因的网络和功能通路将为了解微生物组与宿主动物之间的共生关系提供一个新的水平。我们希望能够识别微生物基因的途径，例如，提供对瘤胃微生物与宿主动物之间的“串扰”的见解，宿主基因组通过该途径控制其自身的瘤胃微生物群。基于这些发现，将制定优化的选择标准和策略，以提高饲料转化率和减少甲烷排放。此外，我们将使用生物标志物来控制微生物基因的选择对瘤胃健康没有不利影响，对动物健康和福利没有潜在影响。我们的大型商业合作伙伴将确保项目成果能够立即在日常育种活动中实施，从而有助于应对粮食安全和动物生产对环境影响的挑战。该项目预计将大大增加宿主动物基因组与瘤胃微生物组之间联系的基础知识，这可能也与包括人类在内的其他物种有关，同时将开发方法和策略，将这些新知识用于动物育种的实际应用。

The Food and Agriculture Organisation of the United Nations has predicted an increase in global meat and milk demand of 76% and 63% by 2050 due to increasing income and growing world population. This will require improved sustainable systems for livestock production. The large fore-gut of cattle, the rumen, contains billions of microbes (the microbiome) per gram of digesta (which is the substance as food undergoes digestion). These microbes ferment human inedible food (e.g. grass) into nutrients the host animal converts into high quality products such as meat and milk. This rumen microbial eco-system is essential for the animal but has one disadvantage for the environment because some microbes produce the potent greenhouse gas methane. This project will address these challenges by using rumen microbial information as animal breeding criteria for improvement of feed conversion efficiency with simultaneous mitigation of methane emissions. In this research we will estimate the extent of the link between animal genome and its rumen microbiome and investigate the causes for their link using a large breeding population. This population is provided by our commercial partner Genus plc and is well structured to ensure accurate estimation of host genetic effects on the microbiome. Our previous research showed that rumen microbial gene abundances are closely related to feed conversion efficiency and methane emissions. However, how and to what extent the host animal genome affects the abundances of microbial genes is unknown and will be investigated within this project. Because the metabolic functions of these microbial genes are mostly known, we expect to identify many novel genetic links between the host animal and specific rumen microbial functions that may even be conserved across species. Networks and functional pathways of rumen microbial genes linked to the animal genome will provide a new level of understanding of the symbiosis between microbiome and host animal. We are expecting to identify pathways of microbial genes, e.g. to provide insight into the "cross-talk" between the rumen microbes and the host animal, being a route by which the host genome controls its own rumen microbiome. Based on these findings, optimised selection criteria and strategies to improve feed conversion ratio and mitigate methane emissions will be developed. In addition, we will use biomarkers to control that there are no adverse effects of selection using microbial genes on rumen health with potential consequences for animal health and welfare. Our large commercial partner will ensure that the outcomes of the project can be immediately implemented in the routine breeding activities and thus contribute to address the challenges of food security and environmental impact of animal production. This project is expected to provide an enormous increase in fundamental knowledge of the links between host animal genome and the rumen microbiome, which may be also relevant in other species including humans, and at the same time will develop methods and strategies to use this new knowledge for practical application in animal breeding.