On-farm CH₄ emissions have been identified as the largest contributors to the carbon footprint of livestock production systems. A requirement to quantify on-farm mitigation under commercial production conditions and a desire to establish the phenotype of thousands of ruminants for breeding programs, has fueled the development of techniques to estimate daily methane production (DMP) from short-term measures of methane concentration or methane flux.The accuracy, precision and applicability of these methods has been largely untested and forms the susbtance of this thesis. In assessing the accuracy of short-term emissions measures to estimate DMP, a high level of concordance was observed between DMP measured over 24h in a respiration chamber (RC) and estimated from multiple short-term measurement estimates using the GreenFeed Emission Monitoring system (GEM). Three independent experiments comparing DMP confirmed that estimates between methods differ by 5% to 8% (P>0.05). This implies that multiple short-term measures of emission rates are complementary to and consistent with respiration chamber-derived measures, providing capability to measure a greater number of animals, potentially in their production environment over extended periods of time. Methane yields (MY; g CH₄/kg DMI) were also derived based on multiple short-term emission measures, with results consistently within 10% of those calculated based on 24h RC data. The overall MY of animals consuming roughages was 21.8g CH₄/kg DMI using GEM data, in keeping with the 22.3g CH₄/kg DMI average in the literature. That implies that GEM units can not only accurately estimate DMP of cattle but also support accurate MY estimates that can be used in quantifying livestock emissions for national greenhouse inventory calculations.

The relationship between rumen microbial ecology and the host is regulated by multiple factors including diet, the microbial inoculum entering the gut, and host genetics. Two hypotheses associated with this statement were developed and tested during this project. The first focused on the relationship between diet, early life microbial inoculum and rumen microbiota and the second concentrated on the association between host genetics and gut microbial ecology. Hypothesis one was that the rumen microbiome of lambs could be altered by post-natal diet and by early-life microbial intervention, to achieve differences in rumen fermentation, development and animal performance that persist beyond weaning. Secondly, it was hypothesized that sheep with different genetic merit for wool growth harbour differences in their rumen microbiome that are associated with differences in gut morphology, physiology, digesta retention time and microbial protein outflow which underpin their wool phenotypes.