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

反刍动物的氮素利用率很低，通常为25%-30%，剩余的氮素通过尿液排泄，部分通过粪便排泄(Huws等人，2018年；Foskolos和Moorby，2018年；Hristov等人，2019年)。当粪便和尿液混合时，氮以氨的形式损失，从而导致陆地富营养化。此外，在泥浆储存期间和土壤应用之后，细菌可以将一部分N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年)。水体中氮的淋失也会导致水体富营养化和生物多样性的丧失。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，低氮使用量对农民来说是一种经济损失。然而，尽管面临这些环境和经济挑战，奶牛一般都会被提供含有过量氮的日粮，这反映了这样一个事实，即从历史上看，大豆等蛋白质来源相对便宜，对更高的牛奶产量有着不懈的关注，以及对奶牛实际蛋白质需求的不确定性。然而，目前的环境和经济挑战意味着，向反刍动物过度喂氮不再可行。因此，迫切需要研究是否能为奶牛提供低氮日粮而不降低生产性能。反刍动物由复杂的胃肠道组成，由网状、瘤胃、皱胃、皱胃和下胃肠道(小肠、盲肠和大肠)组成，其中含有细菌、真菌、原生动物和噬菌体。瘤胃尤其富含微生物，因为这是反刍动物拥有的主要发酵能量收集器官。事实上，如果没有这些瘤胃微生物，宿主将无法生存。因此，瘤胃微生物组对于解决全球农业面临的重大挑战至关重要，包括提高氮效率，因为它在蛋白质分解和氨基酸分解代谢中发挥作用，导致微生物氮，它贡献了十二指肠吸收的蛋白质的60%-90%(Huws等人，2018年)。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是至关重要的，这种方法可以提高反刍动物的产量，同时减少对环境的影响(Yanez-Ruiz等人，2015年)。此外，最近的研究表明，利用氮素效率更高的奶牛也有更好的剩余饲料摄入量(RFI)，即需要更少的饲料才能产生给定的产奶量。来自强化饲料(即低RFI)动物的瘤胃微生物组数据也表明，瘤胃微生物组主要集中在氨基酸新陈代谢上，功能不那么多样化，这表明这些动物专注于氮的利用，这可能是改善饲料的根本原因(Huws等人，2018年)。该项目的假设是，通过更好地理解瘤胃微生物组的作用以及与RFI的联系，可以为奶牛提供含有较低蛋白质水平的日粮，而产奶损失最小，并具有显著的环境效益。该项目的目标是：1.使用体外瘤胃模拟技术评估不同蛋白质水平对奶牛产气量、挥发性脂肪酸、甲烷产量和瘤胃微生物的影响；2.评估奶牛试验中不同蛋白质水平对产奶量、乳成分(包括脂肪酸组成)、身体状况、奶牛健康、日粮消化率以及瘤胃、口腔和粪便微生物群的影响。3.调查氮利用效率和其他生产参数的使用情况，如奶牛消化的傅里叶变换红外光谱、牛奶脂肪酸等。因此，该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