Manipulation of the ruminant gastrointestinal tract microbiomes for reduced environmental impact of nitrogen excretion from dairy cows

反刍动物的氮利用（NUE）很低，通常为25-30%，剩余的氮通过尿液排出，部分通过粪便排出（Huws等人，2018；Foskolos和Moorby.,2018； Hristov等人，2019）。当粪便和尿液混合时，氮以氨的形式流失，导致陆地富营养化。此外，在泥浆储存和随后的土壤施用过程中，部分氮可以被细菌转化为一氧化二氮，这是一种温室气体，其全球变暖潜力是二氧化碳的298倍（Hristov等人，2013）。通过浸出在水道中的氮损失也会导致水生富营养化和生物多样性丧失。除了氮损失对环境的影响外，氮（蛋白质）饲料的成本越来越高，氮的低使用对农民来说是一种经济损失。然而，尽管存在这些环境和经济方面的挑战，奶牛通常被提供含有过量氮的饲料，这反映了这样一个事实，即历史上蛋白质来源（如大豆）相对便宜，对更高产奶量的不懈关注，以及奶牛实际蛋白质需求的不确定性。然而，当前的环境和经济挑战意味着过度喂食氮给反刍动物不再可行。因此，迫切需要进行研究，以确定是否可以在不影响奶牛生产性能的情况下提供低氮日粮。反刍动物由复杂的胃肠道组成，由网状、瘤胃、皱胃、瓣胃和下胃肠道（小肠、盲肠和大肠）组成，是细菌、真菌、原生动物和噬菌体的栖息地。瘤胃尤其富含微生物，因为这是反刍动物主要的发酵能量收集器官。事实上，如果没有这些瘤胃微生物，宿主将无法生存。因此，瘤胃微生物组是解决全球农业面临的重大挑战的核心，包括提高氮肥利用效率，因为它在蛋白质水解和氨基酸分解代谢中发挥作用，产生微生物氮，贡献了十二指肠吸收的60-90%的蛋白质（Huws等，2018）。更好地了解组成微生物所起的作用，对于开发先进的方法来操纵瘤胃微生物群至关重要，从而提高反刍动物产量，同时减少对环境的影响（Yanez-Ruiz et al., 2015）。此外，最近的研究表明，利用氮效率更高的奶牛也有更好的剩余采食量（RFI），即需要更少的饲料来产生给定的产奶量。来自强化饲料（即低RFI）动物的瘤胃微生物组数据也表明，瘤胃微生物组专注于氨基酸代谢，功能多样性较少，这表明这些动物专注于氮的利用，这可能是改良饲料的根本原因（Huws等，2018）。该项目的假设是，通过更好地了解瘤胃微生物组的作用及其与RFI的联系，可以为奶牛提供含有较低蛋白质水平的饲粮，同时使产奶量损失最小，并具有显著的环境效益。这个项目的目标是…采用体外瘤胃模拟技术，评估不同饲粮蛋白质水平对瘤胃产气量、挥发性脂肪酸、甲烷产量和瘤胃微生物的影响；2. 在泌乳奶牛试验中，评估不同蛋白质饲喂水平对产奶量、乳成分（包括脂肪酸谱）、身体状况、奶牛健康、日粮消化率以及瘤胃、口腔和粪便微生物组的影响。研究氮利用效率和其他生产参数的替代指标，如奶牛食糜、乳脂肪酸的红外光谱等。因此，这个项目涵盖了动物科学、微生物学和计算生物学

Nitrogen use (NUE) in ruminants is low, typically 25-30%, with the remaining nitrogen being excreted in urine, and some in the faeces (Huws et al., 2018; Foskolos and Moorby.,2018; Hristov et al., 2019). When faeces and urine mix, N is lost as ammonia which causes terrestrial eutrophication. Furthermore, during slurry storage and following soil application a portion of the N can be converted by bacteria into nitrous oxide, a GHG with a 298-fold greater global warming potential than carbon dioxide (Hristov et al., 2013). Nitrogen loss in waterways via leaching can also cause aquatic eutrophication and biodiversity loss. In addition to the environmental impact of nitrogen losses, nitrogen (protein) feeds are increasingly costly and the low nitrogen use represents an economic loss for farmers. However, despite these environmental and economic challenges, dairy cows are in general offered diets containing excess nitrogen, a reflection of the fact that historically protein sources, such as soya, were relatively cheap to buy, a relentless focus on higher milk yields, and uncertainties about the actual protein requirements of dairy cows. However, current environmental and economic challenges mean that over-feeding nitrogen to ruminants is no longer viable. Therefore, research is urgently required to identify if dairy cows can be offered lower nitrogen diets without loss in performance.Ruminants are composed of a complex gastrointestinal tract, composed of the reticulum, rumen, abomasum, omasum and lower gastrointestinal tract (small intestine, caecum and large intestine), which house bacteria, fungi, protozoa and phage. The rumen, in particular, is rich is microbes as this is the main fermentative energy-harvesting organ possessed by ruminants. Indeed, without these rumen microbes the host would be unable to survive. Consequently, the rumen microbiome is central to addressing the grand challenges facing agriculture globally, including improving NUE, due to its role in proteolysis and catabolism of amino acids, resulting in microbial N, which contributes 60-90% of protein absorbed at the duodenum (Huws et al., 2018). A better understanding of the roles played by the constituent microbes is central to the development of advanced methods to manipulate the rumen microbiome in a manner that improves ruminant production whilst reducing environmental impact (Yanez-Ruiz et al., 2015). Furthermore, recent studies have shown that cows which are more efficient at using nitrogen also have better residual feed intake (RFI), i.e require less feed to produce a given milk yield. Rumen microbiome data from animals with enhanced feed (i.e low RFI) also indicate that the rumen microbiome is focussed in amino acid metabolism and has less diverse functionalities, suggesting that these animals focus on nitrogen utilisation, which may be the underlying reason for the improved feed (Huws et al., 2018).The hypothesis of this project is that, through an improved understanding the role of the rumen microbiome, and the linkages to RFI, dairy cows can be offered diets containing lower protein levels with minimal loss in milk production and with significant environmental benefits. The project aims to 1. Use in vitro rumen-simulating techniques to assess the effects of varying dietary protein level on gas production, volatile fatty acids, methane production and the rumen microbes; 2. Assess the effects of varying protein feeding levels in a lactating dairy cow experiment on milk yield, milk composition (including fatty acid profiles), body condition, cow health, ration digestibility, and the rumen, buccal and faecal microbiome 3. Investigate the use of proxies for nitrogen use efficiency and other production parameters, for example FTIR of dairy cow digesta, milk fatty acids etc. Consequently, this project encompasses animal science, microbiology and computational biology