Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

Holstein Friesian bulls (n = 75) were used to evaluate the effect of restricted and subsequent compensatory growth on muscular and skeletal growth as well as the recovery of carcass and noncarcass components. Fifteen bulls were slaughtered on Day 0 to provide baseline parameters for carcass and noncarcass measurements. Of the remaining 60 bulls, 30 were fed ad libitum (ADLIB) and 30 were fed a restricted (RES) diet to grow at 0.6 kg/d for 125 d, denoted as Period 1. After 125 d of differential feeding, 15 bulls from each group were slaughtered. The remaining bulls in both treatment groups were then offered ad libitum access to feed for a further 55 d (realimentation), denoted as Period 2, after which they were also slaughtered. All animals received the same diet composed of 70% concentrate and 30% grass silage throughout the experimental trial. As planned, feed intake was greater for ADLIB bulls in Period 1 (P < 0.001); however, there was no difference in feed intake during realimentation (P > 0.05). During Period 1, RES bulls gained 0.6 kg/d whereas ADLIB bulls grew at 1.9 kg/d. During realimentation in Period 2, RES bulls displayed accelerated growth, gaining 2.5 kg/d compared with 1.4 kg/d for ADLIB bulls (P < 0.001). This amounted to a live weight difference between treatment groups of 161 kg at the end of Period 1 after restricted feeding, which was then reduced to 84 kg at the end of Period 2 (P < 0.001). Restricted animals achieved a compensatory growth (or recovery) index of 48% within 55 d of realimentation. During Period 2, RES bulls displayed a better feed conversion ratio (P < 0.001) than ADLIB bulls, indicating better feed efficiency. Ultrasonically measured longissmus dorsi growth was greater for ADLIB bulls compared with RES bulls during Period 1; however, this was reversed during Period 2 (P < 0.001). Metabolically active organs such as the liver and components of the gastrointestinal tract were lighter in RES bulls at the end of Period 1, with no difference in the weights of these components after realimentation (P < 0.01). The improved feed efficiency and muscle growth observed during feed restriction induced compensatory growth may be as a consequence of latent effects of reduced requirements of energetically demanding tissues into realimentation.

The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds.

Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.

BackgroundCompensatory growth (CG) is an accelerated growth phenomenon observed in animals upon re-alimentation following a period of dietary restriction. It is typically utilised in livestock systems to reduce feed costs during periods of reduced feed availability. The biochemical mechanisms controlling this phenomenon, however, are yet to be elucidated. This study aimed to uncover the molecular mechanisms regulating the hepatic expression of CG in cattle, utilising RNAseq. RNAseq was performed on hepatic tissue of bulls following 125 days of dietary restriction (RES) and again following 55 days of subsequent re-alimentation during which the animals exhibited significant CG. The data were compared with those of control animals offered the same diet on an ad libitum basis throughout (ADLIB). Elucidation of the molecular control of CG may yield critical information on genes and pathways which could be targeted as putative molecular biomarkers for the selection of animals with improved CG potential.ResultsFollowing a period of differential feeding, body-weight and liver weight were 161 and 4 kg higher, respectively, for ADLIB compared with RES animals. At this time RNAseq analysis of liver tissue revealed 1352 significantly differentially expressed genes (DEG) between the two treatments. DEGs indicated down-regulation of processes including nutrient transport, cell division and proliferation in RES. In addition, protein synthesis genes were up-regulated in RES following a period of restricted feeding. The subsequent 55 days of ad libitum feeding for both groups resulted in the body-weight difference reduced to 84 kg, with no difference in liver weight between treatment groups. At the end of 55 days of unrestricted feeding, 49 genes were differentially expressed between animals undergoing CG and their continuously fed counterparts. In particular, hepatic expression of cell proliferation and growth genes were greater in animals undergoing CG.ConclusionsGreater expression of cell cycle and cell proliferation genes during CG was associated with a 100 % recovery of liver weight during re-alimentation. Additionally, an apparent up-regulation in capacity for cellular protein synthesis during restricted feeding may contribute to and sustain CG during re-alimentation. DEGs identified are potential candidate genes for the identification of biomarkers for CG, which may be incorporated into future breeding programmes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2578-5) contains supplementary material, which is available to authorized users.

Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is exploited worldwide in animal production systems as a method to lower feed costs. However the molecular mechanisms regulated CG expression remain to be elucidated fully. This study aimed to uncover the underlying biology regulating CG in cattle, through an examination of skeletal muscle transcriptional profiles utilising next generation mRNA sequencing technology. Twenty Holstein Friesian bulls were fed either a restricted diet for 125 days, with a target growth rate of 0.6 kg/day (Period 1), following which they were allowed feed ad libitum for a further 55 days (Period 2) or fed ad libitum for the entirety of the trial. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2 respectively and RNAseq analysis was performed. During re-alimentation in Period 2, previously restricted animals displayed CG, growing at 1.8 times the rate of the ad libitum control animals. Compensating animals were also more feed efficient during re-alimentation and compensated for 48% of their previous dietary restriction. 1,430 and 940 genes were identified as significantly differentially expressed (Benjamini Hochberg adjusted P < 0.1) in periods 1 and 2 respectively. Additionally, 2,237 genes were differentially expressed in animals undergoing CG relative to dietary restriction. Dietary restriction in Period 1 was associated with altered expression of genes involved in lipid metabolism and energy production. CG expression in Period 2 occurred in association with greater expression of genes involved in cellular function and organisation. This study highlights some of the molecular mechanisms regulating CG in cattle. Differentially expressed genes identified are potential candidate genes for the identification of biomarkers for CG and feed efficiency, which may be incorporated into future breeding programmes.

The objective of this study was to evaluate the endocrine response and metabolic rate in Holstein–Friesian bulls during restricted feeding and realimentation. Sixty bulls were allocated to 1 of 2 feeding regimes: 1) restricted feed allowance (RES; n = 30) or 2) ad libitum feeding (ADLIB; n = 30) for 125 d (Period 1). The bulls in both treatment groups were then offered ad libitum access to feed for a further 55 d (Period 2). Five and 4 blood samples were collected during periods 1 (n = 60) and 2 (n = 30), respectively. Plasma samples were assayed for hormones and metabolites including insulin, IGF-1, leptin, thyroid hormones, albumin, β-hydroxy butyrate (BHB), creatinine, glucose, NEFA, total protein, triglycerides, and urea. Blood pressure measurements were determined on all animals at the beginning and end of each period as an indicator of metabolic rate. During Period 1, RES bulls gained 0.6 kg/d whereas ADLIB bulls grew at 1.9 kg/d. Following realimentation in Period 2, RES bulls displayed accelerated growth, gaining 2.5 kg/d compared with 1.4 kg/d for ADLIB bulls (P < 0.001). Treatment × period interactions (P < 0.05) were evident for all plasma analytes assayed. During Period 1, RES bulls had lower concentrations of glucose and insulin, reflecting their lower feed intake. Adipose and protein tissue mobilization was evident through greater concentrations of triglycerides, NEFA, BHB, creatinine, albumin, and total protein in RES animals in Period 1. Additionally, the effect of restricted feeding on growth was apparent through lower concentrations of IGF-1. A lower metabolic rate was also apparent through lower concentrations of thyroid hormones and fewer beats per minute in RES bulls during Period 1. During the initial stage of realimentation in Period 2, IGF-1, insulin, thyroid hormones, creatinine, glucose, total protein, and triglycerides followed the same pattern as per Period 1 with divergence maintained between RES and ADLIB bulls (P < 0.05), whereas concentrations of all of these hormones and metabolites had converged between the treatment groups by the end of Period 2. During realimentation, the number of heart beats per minute was greater in RES bulls, indicating greater metabolic rate in these animals (P < 0.001). Results from the current study clearly show that feed restriction followed by realimentation affects key indices of metabolic status as well as tissue catabolism and provides an insight into the metabolic control of compensatory growth in cattle.

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