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

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