Quantitative Differences in Rumen Epithelium Proteins in Lambs Fed Wheat, Perennial Wheat, or Perennial Wheat plus Lucerne.

The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. This research sought to determine if these diets were associated with changes in the membranebound proteins that transport nutrients in the rumen epithelium (RE). Crossbred ewes (Poll Dorset × Merino) were fed W, PW, or PWL (50:50) fresh-cut forage ad libitum for 4 weeks. Average daily gain (ADG; p < 0.001) was highest in the W-fed lambs compared to the PW and PWL. Metabolisable energy intake (MEI) was higher in lambs fed W (p < 0.001) compared to PW and PWL. In pairwise comparisons of the PW and PWL diet group we found protein abundance was significantly (p < 0.05, FDR < 0.05, Benjamini p < 0.05) different in fatty acid metabolism, oxidative phosphorylation, and biosynthesis of cofactors pathways. There were not any differences in protein abundance related to nutrient transport or energy metabolism in the RE between W- vs. PW- and W- vs. PWL-fed lambs. However, in the PW- vs. PWL-fed lambs, there was a difference in the level of proteins regulating the metabolism of fatty acids and energy production in the mitochondria of the rumen epithelium.

Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries).

Methane production from rumen methanogenesis contributes approximately 71% of greenhouse gas emissions from the agricultural sector. This study has performed genomic predictions for methane production from 99 sheep across 3 yr using a residual methane phenotype that is log methane yield corrected for live weight, rumen volume, and feed intake. Using genomic relationships, the prediction accuracies (as determined by the correlation between predicted and observed residual methane production) ranged from 0.058 to 0.220 depending on the time point being predicted. The best linear unbiased prediction algorithm was then applied to relationships between animals that were built on the rumen metabolome and microbiome. Prediction accuracies for the metabolome-based relationships for the two available time points were 0.254 and 0.132; the prediction accuracy for the first microbiome time point was 0.142. The second microbiome time point could not successfully predict residual methane production. When the metabolomic relationships were added to the genomic relationships, the accuracy of predictions increased to 0.274 (from 0.201 when only the genomic relationship was used) and 0.158 (from 0.081 when only the genomic relationship was used) for the two time points, respectively. When the microbiome relationships from the first time point were added to the genomic relationships, the maximum prediction accuracy increased to 0.247 (from 0.216 when only the genomic relationship was used), which was achieved by giving the genomic relationships 10 times more weighting than the microbiome relationships. These accuracies were higher than the genomic, metabolomic, and microbiome relationship matrixes achieved alone when identical sets of animals were used.

Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes.

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.

Carbohydrate transporting membrane proteins of the rumen bacterium, Butyrivibrio proteoclasticus.

The research was aimed at finding which membrane proteins of the rumen bacterium Butyrivibrio proteoclasticus are involved in the uptake of carbohydrates resulting from extracellular enzymatic degradation of hemicellulose and fructan. The proteomic analysis of cells grown with fructose or xylan as the sole substrate identified 13 membrane proteins predicted to function as carbohydrate transporters. One protein detected was the membrane component of a fructose-specific phosphoenolpyruvate:sugar phosphotransferase system believed to be involved in the fructose uptake following extracellular fructan breakdown. The other 12 proteins were all ABC transport system substrate-binding proteins, nine of which belong to functional category COG1653 that includes proteins predicted to transport oligosaccharides. Four of the SBPs were significantly upregulated in xylan grown cells, and three of these were found in polysaccharide utilisation loci where they are clustered with other genes involved in hemicellulose breakdown and metabolism. It is possible that the carbon source available regulates a wider network of genes. The information on the mechanisms used by rumen bacteria to take up carbohydrates from their environment may improve our understanding of the ruminant digestion and facilitate strategies for improved pasture and stored feed utilisation.

Characterisation of host defence proteins in milk using a proteomic approach.

Besides providing nutrition to the newborn, milk also protects the neonate and the mammary gland against infection. As well as the six major proteins, bovine milk contains minor proteins, not all of which have been characterized. In this study, we have subjected bovine skim milk, whey, and milk fat globule membrane (MFGM) fractions to both direct liquid chromatography-tandem mass spectrometry (LC-MS/MS), and two-dimensional electrophoresis (2-DE) followed by matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) of individual protein spots to better characterize the repertoire of minor milk proteins, particularly those involved with host defense. Milk from peak lactation as well as during the period of colostrum formation and during mastitis were analyzed to gain a more complete sampling of the milk proteome. In total, 2903 peptides were detected by LC-MS and 2770 protein spots by 2-DE. From these, 95 distinct gene products were identified, comprising 53 identified through direct LC-MS/MS and 57 through 2-DE-MS. The latter were derived from a total of 363 spots analyzed with 181 being successfully identified. At least 15 proteins were identified that are involved in host defense. These results demonstrate that the proteome of milk is more complex than has previously been reported and a significant fraction of minor milk proteins are involved in protection against infection.