Effects of rumen protozoa on ruminal fermentation, methane (CH4) emissions and nitrogen (N) retention were studied in twelve crossbred ewes given an oaten chaff diet. Over 10 days sheep were progressively adapted to a diet containing 7% coconut oil distillate to suppress rumen protozoa and then were defaunated using sodium 1-(2-sulfonatooxyethoxy) dodecane (Empicol). Twelve weeks after defaunation treatment, five sheep were inoculated with rumen fluid collected from cannulated sheep to refaunate them and that the effect of re-establishment of rumen protozoa 0, 7, 14 and 21 days following refaunation on ruminal fermentation and CH4 emissions was examined in Experiment 1. As a following study (Experiment 2), feed intake was restricted to 1.5 x ME requirement for maintenance from day 28 to day 43 when dry matter (DM) digestibility, N retention, fermentation and CH4 emissions were compared between defaunated and refaunated sheep. Sheep were scanned through a computed tomography scanner on day 0 and day 28 to estimate reticulo-rumen (RR) weight and carcass composition. It was concluded that refaunated sheep did not have a higher daily CH4 production (DMP, g CH4/day) than did the defaunated cohort within 21 days after refaunation as measured by Greenfeed Emission Monitoring units. Total volatile fatty acid (VFA) concentration and the proportion of propionate in the rumen VFA gradually increased over 21 days following refaunation (Experiment 1), while a change towards higher butyrate and lower acetate proportions was observed after 28 days (Experiment 2; P<0.05). There was a tendency towards a heavier RR weight (P=0.08) and a higher ratio of RR to liveweight in defaunated sheep 28 days after refaunation (P < 0.001), but carcass composition was not affected by refaunation status. Experiment 2 showed defaunated sheep had a 7% lower DMP than did refaunated sheep with an established rumen fauna (P<0.05). Apparent whole-tract N and DM digestibility and microbial crude protein supply were not different between defaunated and refaunated sheep, while energy losses in CH4 (MJ/day) and CH4 as a proportion of gross energy intake were both approximately 8% lower in defaunated sheep. The reduced CH4 emissions achieved by defaunation occurred without altering total VFA, apparent whole-tract N and DM digestibility or ADG.

Ruminant livestock contribute to atmospheric methane (CH₄) from enteric microbial fermentation of feed in the reticulo-rumen. Our research aimed to increase understanding of how digestive characteristics and rumen anatomy of the host animal contribute to variation in CH₄ emissions between individual sheep. In total, 64 ewes were used in an incomplete block experiment with four experimental test periods (blocks). Ewes were chosen to represent the diversity of phenotypic variation in CH₄ emissions: there were at least 10 offspring from each of four sires and a range of liveweights. Throughout the experiment, the ewes were fed equal parts of lucerne and oaten chaff, twice daily, at 1.5 times the maintenance requirements. Daily CH₄ emission (g/day) increased significantly (P < 0.001) with an increasing dry-matter intake (DMI) and reticulo-rumen volume (P < 0.001). Lower methane yield (g CH₄/kg DMI) was associated with shorter mean retention times of liquid (r = 0.59; P < 0.05) and particle (r = 0.63; P < 0.05) phases of the digesta in the rumen. Significant between sire variation was observed in CH₄ emissions and in rumen volume (P = 0.02), the masses of liquids (P = 0.009) and particles (P < 0.03) in the rumen and the proportion of gas in the dorsal sac of the rumen (P = 0.008). The best predictors of variation in CH₄ emissions due to the host were DMI, CO₂ emissions, rumen volume, liveweight, mean retention time of particles in the rumen, dorsal papillae density and the proportion of liquid in the contents of the rumen compartments.

Livestock produce 10% of the total CO₂-equivalent greenhouse gases in Australia, predominantly as methane from rumen fermentation. Genetic selection has the potential to reduce emissions and be adopted in Australian grazing systems. Developing a breeding objective for reduced methane emissions requires information about heritability, genetic relationships, when best to measure the trait and knowledge of the annual production of methane. Among- and within-animal variation in methane production, methane yield and associated traits were investigated, so as to determine the optimal time of measurement and the relationship between that measurement and the total production of methane. The present study measured 96 ewes for methane production, liveweight, feed intake, rumen volume and components, and volatile fatty acid (VFA) production and composition. Measurements were recorded at three ages and different physiological states, including growing (12 months), dry and pregnant (21 months) and dry (non-pregnant, non-lactating; 28 months of age). The single biggest determinant of methane production was feed intake, but there were additional effects of age, proportion of propionate to (acetate+butyrate) in rumen VFA, total VFA concentration and CO₂ flux. Rumen volume and pregnancy status also significantly affected methane production. Methane production, CO₂ flux, liveweight, feed intake and rumen volume had high repeatability (>65%), but repeatability of methane yield and VFA traits were low (<20%). There were no interactions between sire and age (or pregnancy status) for methane traits. This suggests that methane could be measured at any time in the production cycle. However, because MY is reduced during pregnancy, it might be best to measure methane traits in dry ewes (neither pregnant nor lactating).

Ruminants are significant contributors to the livestock generated component of the greenhouse gas, methane (CH₄). The CH₄ is primarily produced by the rumen microbes. Although the composition of the diet and animal intake amount have the largest effect on CH₄ production and yield (CH₄ production/dry matter intake, DMI), the host also influences CH₄ yield. Shorter rumen feed mean retention time (MRT) is associated with higher dry matter intake and lower CH₄ yield, but the molecular mechanism(s) by which the host affects CH₄ production remain unclear. We integrated rumen wall transcriptome data and CH₄ phenotypes from two independent experiments conducted with sheep in Australia (AUS, n = 62) and New Zealand (NZ, n = 24). The inclusion of the AUS data validated the previously identified clusters and gene sets representing rumen epithelial, metabolic and muscular functions. In addition, the expression of the cell cycle genes as a group was consistently positively correlated with acetate and butyrate concentrations (p < 0.05, based on AUS and NZ data together). The expression of a group of metabolic genes showed positive correlations in both AUS and NZ datasets with CH₄ production (p < 0.05) and yield (p < 0.01). These genes encode key enzymes in the ketone body synthesis pathway and included members of the poorly characterized aldo-keto reductase 1C (AKR1C ) family. Several AKR1C family genes appear to have ruminant specific evolution patterns, supporting their specialized roles in the ruminants. Combining differential gene expression in the rumen wall muscle of the shortest and longest MRT AUS animals (no data available for the NZ animals) with correlation and network analysis, we identified a set of rumen muscle genes involved in cell junctions as potential regulators of MRT, presumably by influencing contraction rates of the smooth muscle component of the rumen wall. Higher rumen expression of these genes, including SYNPO (synaptopodin, p < 0.01) and NEXN (nexilin, p < 0.05), was associated with lower CH₄ yield in both AUS and NZ datasets. Unlike the metabolic genes, the variations in the expression of which may reflect the availability of rumen metabolites, the muscle genes are currently our best candidates for causal genes that influence CH₄ yield.