Understanding the interactive role of the rumen microbiome with diet and enteric emissions in cattle

Enteric methane (CH4), produced by members of the microbial population residing in the rumen of domesticated livestock, is accountable for ~6% of global greenhouse gas (GHG) emissions. In a bid to develop cost effect dietary and breeding based mitigation strategies for the livestock industry, a series of studies that utilised 16S ribosomal RNA (rRNA) amplicon sequencing to investigate the relationship of the rumen microbiota with diet and enteric CH4 emissions in cattle, were investigated as part of this thesis. In addition, this thesis aimed to optimise the bioinformatics analysis of rumen microbial amplicon sequencing data. With the use of a rumen specific amplicon sequencing standard, the taxonomic classification of rumen microbial amplicon sequence data amongst the main 16S rRNA databases was evaluated in Chapter 3. In Chapter 4, 16S rRNA amplicon sequencing was utilised to investigate the impacts of including white clover in the grazing sward on the rumen bacterial and archaeal populations of dairy cows. The CH4 abatement potential of supplementing concentrates, solely formulated from industrial plant based by-products (BP), to a pastoral based diet, was explored in Chapter 5. The benefits of utilising the residual CH4 emissions (RME) concept to determine the methanogenic output of ruminant livestock, independent of animal productivity, and the impacts ranking animals in terms of RME on the rumen microbiota, was investigated in Chapter 6 and 7. In Chapter 3, the benefits of utilising a rumen specific amplicon sequencing standard to optimise 16s rRNA amplicon analysis was illustrated, with the results obtained implemented during the rumen microbial analysis conducted in Chapters 4, 5 and 7. Results from Chapter 4 highlighted a subtle change to the composition of the grazing sward, associated with the inclusion of white clover, resulted in an increased ruminal abundance of the pectin degrading bacteria Lachnospira and methylotrophic archaea Methanosphaera. A reduced abundance of the Firmicutes phyla, yet lack of an effect on the rumen methanogen community, and a ~20% lower CH4 output, was observed with the supplementation of a pastoral based diet with a high fat and fibre BP concentrate formulation, in comparison to a cereal based ration, in vitro. Comparable levels of animal performance but a ~30% difference in all measures of enteric CH4 emissions, and alteration to the rumen fermentation profile, was observed in beef cattle ranked as high and low for RME, in Chapter 6. In Chapter 7, a small cohort of bacterial genera involved in the acrylate pathway and methanogens indicative of a reduced synthesis of dihydrogen (H2) in the rumen, were identified as potential rumen microbial biomarkers for a low RME phenotype. In conclusion, data generated as part of this thesis emphasised the mitigation potential of novel dietary and animal breeding based strategies and provides a baseline assessment of the relationship of the rumen microbiota with diet and enteric CH4 emissions in cattle. This information will guide the future metagenomics and metatranscriptomic attempts to better understand the influence of the ruminant host on prevailing conditions within the rumen and methanogenesis.