Understanding the role of the rumen microbiome for enhancing feed efficiency and reducing methane emissions in sheep

Abstract

Sheep play a vital role in global agricultural enterprises and support human livelihoods by converting human-inedible plant matter into human-edible products, such as meat and milk. However, the production of methane, a potent greenhouse gas, during the fermentation of feed by sheep's rumen microbiome contributes to anthropogenic greenhouse gas emissions. Therefore, the primary objective of this thesis was to investigate the role of the rumen microbiome in sheep to enhance feed utilisation, reduce methane emissions to promote the long-term sustainability of the sector. Chapter 2 of this thesis used 16S rRNA amplicon sequencing to investigate the bacterial and archaeal populations in both solid and liquid fractions of the rumen of sheep with different feed conversion rates. The study found that the rumen archaea diversity and composition differed between feed efficient cohorts, providing evidence for the link between methane production and dietary energy loss. Chapter 3 explored the impact of breed on the bacterial and archaeal populations in the solid, liquid, and epithelial rumen fractions of sheep using 16S rRNA amplicon sequencing. The study found that breed influenced feed efficiency and the rumen bacterial populations, with potential applications for breeding programs aimed at selecting microbiomes that can utilise feed efficiently and produce less methane. The study also found variations in the distribution of bacterial taxa between ruminal fractions, revealing a rumen fraction bias that has implications for sheep rumen sampling techniques. Chapter 4 used PACs to investigate the effect of time off feed (TOF) on methane emissions and employed meta-omics techniques to assess the influence of TOF on rumen bacterial and archaeal communities in pasture-grazed sheep. The study found that TOF can influence methane emissions and the composition of the rumen microbiome, which could have implications for methane-microbiome studies involving animals that spend variable amounts of time off feed. Overall, this thesis showed that the rumen microbiome is influenced by a range of factors such as feed efficiency, breed, ruminal fraction, and time off feed, with potential implications for improving feed conversion efficiency, reducing methane emissions, and optimising rumen sampling techniques.