Cattle selected for lower residual feed intake have reduced daily methane production

Compilations and updates on residual feed intake in sheep

The increasing global demand for food and the strong effect of climate change have forced animal science to advance regarding new methods of selection in search of more efficient animals in production systems. Feed consumption represents more than 70% of the costs of sheep farms, and more efficient animals can increase the farmers' profitability. One of the main measures of feed efficiency is estimated residual feed intake (RFI), created in 1963 by Robert Koch for estimation in cattle and later adapted for sheep. Animals with negative RFI values (RFI-) are more efficient than animals with positive values (RFI+), with influence on the variables of performance, carcass quality and production of enteric gases. The RFI is the most common and accepted metric of the feed efficiency trait for genetic selection, since it is independent of growth traits, unlike the feed conversion ratio. The purpose of this review article was to present updated literature information on the relationship of RFI estimates with performance measures, molecular markers, greenhouse gas production and feed efficiency, the technical aspects and physiological basis of metabolic in sheep.

Longitudinal modeling of residual carbon dioxide and residual feed intake in the Nordic Red dairy cattle

Feed utilization efficiency is an important trait in dairy production playing a significant role in reducing feed costs and lowering methane emission. One of the metrics used to measure feed efficiency in dairy cows is residual feed intake (RFI). This metric requires routine measurement of feed intake. Since there is a positive high correlation between heat production and carbon dioxide (CO2) production on the one hand and heat production and efficiency on the other hand, residual carbon dioxide (RCO2) might be a useful metric to improve feed efficiency. The objectives of this study were to model the trajectories of RCO2 and RFI as well as to estimate their repeatabilities and correlations at different stages of lactation. Daily CO2 output and feed intake were recorded from 46 primiparous Nordic Red dairy cows using two Greenfeed Emissions Monitoring™ systems from 2 to 305 days in milk (DIM). Edited data comprised 5 995 daily averages. To calculate predicted values of CO2 and DM intake (DMI), prediction models were developed by fitting multiple regression models to observations. Subsequently, RCO2 and RFI were calculated by subtracting predicted values of CO2 and DMI from their corresponding actual observations. A random regression bivariate model was fitted to estimate repeatabilities and animal correlations within lactation at different DIMs between RCO2 and RFI traits. The model fitted included fixed effects of year-month of recording, lactation month, fixed regressions as well as random regressions for the animal effect. The residual variance was considered to be heterogeneous. Repeatabilities and animal correlations of RCO2 and RFI between selected DIM (for every 30 DIM i.e., 6, 36,…, 246 and 276) were calculated. Repeatability of RCO2 was high at the beginning of lactation (0.72 at DIM 6) and decreased around the peak of milk production (0.27 at DIM 96) and again increased gradually toward the end of lactation. Similarly, RFI also had high repeatability at the beginning (0.86 at DIM 6); however, it decreased in mid-lactation (0.37 at DIM 156) and then increased toward the end of lactation. Animal correlations between RCO2 and RFI were moderate to high on the same DIM and ranged from 0.37 to 0.88. Overall, we found that animals with higher CO2 production than expected also consume more DMI than expected, but the moderate correlation between RCO2 and RFI found in this study calls for more research to assess the potential of RCO2 to become a new feed efficiency metric.

Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes

We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.

Residual feed intake is related to metabolic and inflammatory response during the preweaning period in Italian Simmental calves

Residual Feed Intake (RFI) is defined as the difference between measured and predicted intake. Understanding its biological regulators could benefit farm profit margins. The most-efficient animals (M-Eff) have observed intake smaller than predicted resulting in negative RFI, whereas the least-efficient (L-Eff) animals have positive RFI. Hence, this observational study aimed at retrospectively comparing the blood immunometabolic profile in calves with divergent RFI during the preweaning period. Twenty-two Italian Simmental calves were monitored from birth through 60 d of age. Calves received 3 L of colostrum from their respective dams. From 2 to 53 d of age, calves were fed a milk replacer twice daily, whereas from 54 to 60 d (i.e., weaning) calves were stepped down to only one meal in the morning. Calves had ad libitum access to concentrate and intakes were recorded daily. The measurement of BW and blood samples were performed at 0, 1, 7, 14, 21, 28, 35, 45, 54, and 60 d of age. Calves were ranked and categorized as M-Eff or L-Eff according to the median RFI value. Median RFI was -0.06 and 0.04 kg of DMI/d for M-Eff and L-Eff, respectively. No evidence for group differences was noted for colostrum and plasma IgG concentrations. Although growth rate was not different, as expected, (0.67 kg/d [95% CI = 0.57-0.76] for both L-Eff and M-Eff) throughout the entire preweaning period (0-60 d), starter intake was greater in L-Eff compared with M-Eff calves (+36%). Overall, M-Eff calves had a greater gain-to-feed ratio compared with L-Eff calves (+16%). Plasma ceruloplasmin, myeloperoxidase, and reactive oxygen metabolites concentrations were greater in L-Eff compared with M-Eff calves. Compared with L-Eff, M-Eff calves had an overall greater plasma concentration of globulin, and γ-glutamyl transferase (indicating a better colostrum uptake) and Zn at 1 d. Retinol and urea were overall greater in L-Eff. The improved efficiency in nutrient utilization observed in M-Eff was paired with a lower grade of oxidative stress and systemic inflammation. L-Eff may have had greater energy expenditure to support the activation of the immune system.

Climate change and dairy farming sustainability; a causal loop paradox and its mitigation scenario

It is arguable at this time whether climate change is a cause or effect of the disruption in dairy farming. Climate change drastically affects the productive performance of livestock, including milk and meat production, and this could be attributed to the deviation of energy resources towards adaptive mechanisms. However, livestock farming also contributes substantially to the existing greenhouse gas pool, which is the causal of the climate change. We gathered relevant information from the recent publication and reviewed it to elaborate on sustainable dairy farming management in a changing climatic scenario, and efforts are needed to gather this material to develop methods that could help to overcome the adversities associated with livestock industries. We summarize the intervention points to reverse these adversities, such as application of genetic technology, nutrition intervention, utilization of chemical inhibitors, immunization, and application of metagenomics, which may help to sustain farm animal production in the changing climate scenario.

Intake, digestibility, energy and nitrogen utilisation, and enteric methane emission in Holstein and Girolando-F1 cows during the transition period

This study aimed to evaluate intake, energy and nitrogen balance as well as methane emission in Holstein and ½ Holstein ½ Gyr (Girolando-F1) cows during the transition period. Twenty-four cows (12 Holstein and 12 Girolando-F1) were used to evaluate feed intake, apparent digestibility, heat production and methane emission, carried out in two periods: from 28 to 19 days pre-calving and from 15 to 23 days post-calving. A completely randomised design was used and data were analysed by ANOVA within periods (pre- and post-calving) considering the main effect of genetic groups. Girolando-F1cows presented greater body condition score (BCS) compared with Holstein. During pre-calving, there were no differences between genetic groups, except for highest heat production per kilogram of metabolic body weight for Holstein cows. After calving, Holstein cows had greater intake of DM, nitrogen, NDF per kg of BW and produced more heat per kg of metabolic body weight. Holstein cows yielded more milk and fat-corrected milk (FCM4%) compared with Girolando-F1 cows. Holstein cows presented higher methane emission per unit of BW and of metabolic weight. Emissions of enteric methane per kilogram of milk and per kilogram of FCM4% tended to be lower for Holstein compared with Girolando-F1 cows. Nitrogen and energy retention were similar for both Holstein and Girolando-F1 at pre- and post-calving. Despite differences in BCS, DMI, and milk yield, Girolando-F1 and Holstein cows present overall similar energy efficiency, albeit Holstein cows tended to present less methane emission per kg of eligible product (milk).

Evolving understanding of rumen methanogen ecophysiology

Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.

Different nutritional systems influence the tenderness and lipid oxidation of ewe lamb meat without altering gene expression

Feeding is a determining factor in the various characteristics of sheep meat and animal performance, the objectives were to evaluate the effect of supplementation of ewe lambs finished in different nutritional planes on the gene expression of CASP3, CAPN1, CAPN2 and CAST and its possible association with meat quality. Samples of the Longissimus lumborum muscle of 24 ewe lambs were used, distributed in 3 groups (n=8): P (pasture), PS (pasture and supplement) and F (feedlot). Physicochemical analyses were performed for centesimal analysis, pH, lipid oxidation, Warner-Bratzler shear force and RT-qPCR for the analysis of relative gene expression of the following genes: CASP3, CAPN1, CAPN2 and CAST. There is an increase in daily weight gain and ethereal extract values in the meat of confined animals, due to the greater energy intake in the nutrition of these animals. Animals kept only on pasture have lower lipid oxidation in meat than other treatments because of the lower percentage of lipids. The Warner-Bratzler shear force is considerably higher in the meat of animals kept only on pasture but is still considered tender. The different nutritional systems do not interfere with the gene expression of CASP3, CAPN1, CAPN2 and CAST in ewe lambs.

Analysis of liver miRNA in Hu sheep with different residual feed intake

Feed efficiency (FE), an important economic trait in sheep production, is indirectly assessed by residual feed intake (RFI). However, RFI in sheep is varied, and the molecular processes that regulate RFI are unclear. It is thus vital to investigate the molecular mechanism of RFI to developing a feed-efficient sheep. The miRNA-sequencing (RNA-Seq) was utilized to investigate miRNAs in liver tissue of 6 out of 137 sheep with extreme RFI phenotypic values. In these animals, as a typical metric of FE, RFI was used to distinguish differentially expressed miRNAs (DE_miRNAs) between animals with high (n = 3) and low (n = 3) phenotypic values. A total of 247 miRNAs were discovered in sheep, with four differentially expressed miRNAs (DE_miRNAs) detected. Among these DE_miRNAs, three were found to be upregulated and one was downregulated in animals with low residual feed intake (Low_RFI) compared to those with high residual feed intake (High_RFI). The target genes of DE_miRNAs were primarily associated with metabolic processes and biosynthetic process regulation. Furthermore, they were also considerably enriched in the FE related to glycolysis, protein synthesis and degradation, and amino acid biosynthesis pathways. Six genes were identified by co-expression analysis of DE_miRNAs target with DE_mRNAs. These results provide a theoretical basis for us to understand the sheep liver miRNAs in RFI molecular regulation.

Genomic evaluation of feed efficiency in US Holstein heifers

There is growing interest in improving feed efficiency traits in dairy cattle. The objectives of this study were to estimate the genetic parameters of residual feed intake (RFI) and its component traits [dry matter intake (DMI), metabolic body weight (MBW), and average daily gain (ADG)] in Holstein heifers, and to develop a system for genomic evaluation for RFI in Holstein dairy calves. The RFI data were collected from 6,563 growing Holstein heifers (initial body weight = 261 ± 52 kg; initial age = 266 ± 42 d) for 70 d, across 182 trials conducted between 2014 and 2022 at the STgenetics Ohio Heifer Center (South Charleston, OH) as part of the EcoFeed program, which aims to improve feed efficiency by genetic selection. The RFI was estimated as the difference between a heifer's actual feed intake and expected feed intake, which was determined by regression of DMI against midpoint MBW, age, and ADG across each trial. A total of 61,283 SNPs were used in genomic analyses. Animals with phenotypes and genotypes were used as training population, and 4 groups of prediction population, each with 2,000 animals, were selected from a pool of Holstein animals with genotypes, based on their relationship with the training population. All traits were analyzed using univariate animal model in DMU version 6 software. Pedigree information and genomic information were used to specify genetic relationships to estimate the variance components and genomic estimated breeding values (GEBV), respectively. Breeding values of the prediction population were estimated by using the 2-step approach: deriving the prediction equation of GEBV from the training population for estimation of GEBV of prediction population with only genotypes. Reliability of breeding values was obtained by approximation based on partitioning a function of the accuracy of training population GEBV and magnitudes of genomic relationships between individuals in the training and prediction population. Heifers had DMI (mean ± SD) of 8.11 ± 1.59 kg over the trial period, with growth rate of 1.08 ± 0.25 kg/d. The heritability estimates (mean ± SE) of RFI, MBW, DMI, and growth rate were 0.24 ± 0.02, 0.23 ± 0.02, 0.27 ± 0.02, and 0.19 ± 0.02, respectively. The range of genomic predicted transmitted abilities (gPTA) of the training population (-0.94 to 0.75) was higher compared with the range of gPTA (-0.82 to 0.73) of different groups of prediction population. Average reliability of breeding values from the training population was 58%, and that of prediction population was 39%. The genomic prediction of RFI provides new tools to select for feed efficiency of heifers. Future research should be directed to find the relationship between RFI of heifers and cows, to select individuals based on their lifetime production efficiencies.

Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host

BACKGROUND

Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.

RESULTS

Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.

CONCLUSIONS

Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.

Replacing Fertilizer with Dried Distillers' Grains in Stocker Cattle Systems on Southern Great Plains Old World Bluestem, USA

The objective was to examine the effects of dried distillers' grains supplementation and fertilization strategies on the cattle performance and resource use efficiency of stocker cattle grazing on Plains Old World bluestem. Over 4 consecutive years, heifers and steers (average n = 239) were randomly assigned to 1 of 4 treatments: (1) low input, low stocking density, and no fertilizer or distillers grains supplementation (LOW); (2) high stocking density and no fertilizer with distillers grains supplementation (DDGS); (3) high stocking density and 90 kg of nitrogen/ha with no distillers grains supplementation (NFERT); (4) high stocking density, 90 kg of nitrogen/ha, and 39 kg of phosphorus/ha with no distillers grains supplementation (NPFERT). Cattle grazed in the pastures from mid-May to mid-September each year, except for 2011, when the experiment ended in July due to lack of forage. Data were analyzed using a linear model with fixed effects of treatment, year, and treatment × year (R software). Nitrogen use efficiency (retained/inputs) was affected by a treatment × year interaction, where LOW had the greatest efficiency in all years and DDGS was greater than NFERT and NPFERT in all years except 2012, with NFERT and NPFERT being not different in all years. The estimated total carbon equivalent emissions were greater for DDGS, NFERT, and NPFERT than LOW, but the carbon footprint (kg CO2eq/kg weight gain) was lesser for LOW and DDGS, which were not different, than NFERT and NPFERT, which were also not different. Replacing nitrogen fertilizer with dried distiller's grains improved the cattle performance and the efficiency of resource use, and could be a viable economic alternative to traditional systems.

Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer

There has been little information about the proteome of bovine faeces or about the contribution to the faecal proteome of proteins from the host, the feed or the intestinal microbiome. Here, the bovine faecal proteome and the origin of its component proteins was assessed, while also determining the effect of treating barley, the major carbohydrate in the feed, with either ammonia (ATB) or sodium propionate (PTB) preservative. Healthy continental crossbreed steers were allocated to two groups and fed on either of the barley-based diets. Five faecal samples from each group were collected on Day 81 of the trial and analysed by quantitative proteomics using nLC-ESI-MS/MS after tandem mass tag labelling. In total, 281 bovine proteins, 199 barley proteins, 176 bacterial proteins and 190 archaeal proteins were identified in the faeces. Mucosal pentraxin, albumin and digestive enzymes were among bovine proteins identified. Serpin Z4 a protease inhibitor was the most abundant barley protein identified which is also found in barley-based beer, while numerous microbial proteins were identified, many originating bacteria from Clostridium, while Methanobrevibacter was the dominant archaeal genus. Thirty-nine proteins were differentially abundant between groups, the majority being more abundant in the PTB group compared to the ATB group. SIGNIFICANCE: Proteomic examination of faeces is becoming a valuable means to assess the health of the gastro-intestinal tract in several species, but knowledge on the proteins present in bovine faeces is limited. This investigation aimed to characterise the proteome of bovine faecal extracts in order to evaluate the potential for investigations of the proteome as a means to assess the health, disease and welfare of cattle in the future. The investigation was able to identify proteins in bovine faeces that had been (i) produced by the individual cattle, (ii) present in the barley-based feed eaten by the cattle or (iii) produced by bacteria and other microbes in the rumen or intestines. Bovine proteins identified included mucosal pentraxin, serum albumin and a variety of digestive enzymes. Barley proteins found in the faeces included serpin Z4, a protease inhibitor that is also found in beer having survived the brewing process. Bacterial and archaeal proteins in the faecal extracts were related to several pathways related to the metabolism of carbohydrates. The recognition of the range of proteins that can be identified in bovine faeces raises the possibility that non-invasive sample collection of this material could provide a novel diagnostic approach to cattle health and welfare.

Plasma and milk metabolomics in lactating sheep divergent for feed efficiency

Enhancing the ability of animals to convert feed into meat or milk by optimizing feed efficiency (FE) has become a priority in livestock research. Although untargeted metabolomics is increasingly used in this field and may improve our understanding of FE, no information in this regard is available in dairy ewes. This study was conducted to (1) discriminate sheep divergent for FE and (2) provide insights into the physiological mechanisms contributing to FE through high-throughput metabolomics. The ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF-MS) technique was applied to easily accessible animal fluids (plasma and milk) to assess whether their metabolome differs between high- and low-feed efficient lactating ewes (H-FE and L-FE groups, respectively; 8 animals/group). Blood and milk samples were collected on the last day of the 3-wk period used for FE estimation. A total of 793 features were detected in plasma and 334 in milk, with 100 and 38 of them, respectively, showing differences between H-FE and L-FE. The partial least-squares discriminant analysis separated both groups of animals regardless of the type of sample. Plasma allowed the detection of a greater number of differential features; however, results also supported the usefulness of milk, more easily accessible, to discriminate dairy sheep divergent for FE. Regarding pathway analysis, nitrogen metabolism (either anabolism or catabolism) seemed to play a central role in FE, with plasma and milk consistently indicating a great impact of AA metabolism. A potential influence of pathways related to energy/lipid metabolism on FE was also observed. The variable importance in the projection plot revealed 15 differential features in each matrix that contributed the most for the separation in H-FE and L-FE, such as l-proline and phosphatidylcholine 20:4e in plasma or l-pipecolic acid and phosphatidylethanolamine (18:2) in milk. Overall, untargeted metabolomics provided valuable information into metabolic pathways that may underlie FE in dairy ewes, with a special relevance of AA metabolism in determining this complex phenotype in the ovine. Further research is warranted to validate these findings.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Predicting dry matter intake in beef cattle

Technology that facilitates estimations of individual animal dry matter intake (DMI) rates in group-housed settings will improve production and management efficiencies. Estimating DMI in pasture settings or facilities where feed intake cannot be monitored may benefit from predictive algorithms that use other variables as proxies. This study examined the relationships between DMI, animal performance, and environmental variables. Here we determined whether a machine learning approach can predict DMI from measured water intake variables, age, sex, full body weight, and average daily gain (ADG). Two hundred and five animals were studied in a drylot setting (152 bulls for 88 d and 53 steers for 50 d). Collected data included daily DMI, water intake, daily predicted full body weights, and ADG using In-Pen-Weighing Positions and Feed Intake Nodes. After exclusion of 26 bulls of low-frequency breeds and one severe (>3 standard deviations) outlier, the final number of animals used for modeling was 178 (125 bulls, 53 steers). Climate data were recorded at 30-min intervals throughout the study period. Random Forest Regression (RFR) and Repeated Measures Random Forest (RMRF) were used as machine learning approaches to develop a predictive algorithm. Repeated Measures ANOVA (RMANOVA) was used as the traditional approach. Using the RMRF method, an algorithm was constructed that predicts an animal's DMI within 0.75 kg. Evaluation and refining of algorithms used to predict DMI in drylot by adding more representative data will allow for future extrapolation to controlled small plot grazing and, ultimately, more extensive group field settings.

Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems

Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH₄), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H₂ and CO₂), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH₄-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH₄ mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.

Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle

BACKGROUND

Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs.

RESULTS

The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10).

CONCLUSION

Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.

Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle

Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets.

Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH₄) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers.

Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH₄ emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH₄ emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.

Effects of a Moderate or Aggressive Implant Strategy on the Rumen Microbiome and Metabolome in Steers

The effects of growth-promoting implants have been well-defined for their ability to impact growth performance in beef cattle. Production-relevant microbes and microbiomes in the rumen have also been associated with growth traits. However, the role of implants on the rumen microbiome has not been determined. The objective of this study was to determine if different doses of implant hormones cause gain-associated ruminal microbial community changes. To assess this, a completely randomized design was used and 336 fall-born steers 450 to 470 days of age from the germplasm evaluation population at the US Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy (n = 167) of Revalor-IS (80 mg trenbolone acetate and 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate and 24 mg estradiol) or 2) an aggressive implant strategy (n = 169) of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate and 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% vitamin and mineral supplement, and 0.75% urea, on a DM basis). On d 85 after implants administration, rumen contents were collected via orogastric tubing. Samples were sequenced to target and identify bacteria, archaea, and protozoa. Untargeted metabolomics was performed on rumen content using ultra high performance liquid chromatography high resolution mass spectrometry. Production data between implant strategies was analyzed using a mixed model ANOVA (SASv9.4, Cary, NC) followed by separation of least squares means. Microbial diversity between strategies did not differ for archaea or protozoa (P &gt; 0.05). Average daily gain was different (P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated with implant strategy. Two metabolites, N-acetyllysine and N-acetylornithine, were found in greater abundance in the moderate implant strategy (P ≤ 0.04). Understanding associations between the rumen microbiome and implant strategies may allow improvement of growth efficiency in beef cattle.

Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase

The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle.

Selecting for Feed Efficient Cows Will Help to Reduce Methane Gas Emissions

In the last decade, several countries have included feed efficiency (as residual feed intake; RFI) in their breeding goal. Recent studies showed that RFI is favorably correlated with methane emissions. Thus, selecting for lower emitting animals indirectly through RFI could be a short-term strategy in order to achieve the intended reduction set by the EU Commission (-55% for 2030). The objectives were to 1) estimate genetic parameters for six methane traits, including genetic correlations between methane traits, production, and feed efficiency traits, 2) evaluate the expected correlated response of methane traits when selecting for feed efficiency with or without including methane, 3) quantify the impact of reducing methane emissions in dairy cattle using the Danish Holstein population as an example. A total of 26,664 CH4 breath records from 647 Danish Holstein cows measured over 7 years in a research farm were analyzed. Records on dry matter intake (DMI), body weight (BW), and energy corrected milk (ECM) were also available. Methane traits were methane concentration (MeC, ppm), methane production (MeP; g/d), methane yield (MeY; g CH4/kg DMI), methane intensity (MeI; g CH4/kg ECM), residual methane concentration (RMeC), residual methane production (RMeP, g/d), and two definitions of residual feed intake with or without including body weight change (RFI1, RFI2). The estimated heritability of MeC was 0.20 ± 0.05 and for MeP, it was 0.21 ± 0.05, whereas heritability estimates for MeY and MeI were 0.22 ± 0.05 and 0.18 ± 0.04, and for the RMeC and RMeP, they were 0.23 ± 0.06 and 0.16 ± 0.02, respectively. Genetic correlations between methane traits ranged from moderate to highly correlated (0.48 ± 0.16–0.98 ± 0.01). Genetic correlations between methane traits and feed efficiency were all positive, ranging from 0.05 ± 0.20 (MeI-RFI2) to 0.76 ± 0.09 (MeP-RFI2). Selection index calculations showed that selecting for feed efficiency has a positive impact on reducing methane emissions’ expected response, independently of the trait used (MeP, RMeP, or MeI). Nevertheless, adding a negative economic value for methane would accelerate the response and help to reach the reduction goal in fewer generations. Therefore, including methane in the breeding goal seems to be a faster way to achieve the desired methane emission reductions in dairy cattle.

Enteric Methane Emissions and Animal Performance in Dairy and Beef Cattle Production: Strategies, Opportunities, and Impact of Reducing Emissions

Enteric methane (CH4) emissions produced by microbial fermentation in the rumen resulting in the emission of greenhouse gases (GHG) into the atmosphere. The GHG emissions reduction from the livestock industry can be attained by increasing production efficiency and improving feed efficiency, by lowering the emission intensity of production, or by combining the two. In this work, information was compiled from peer-reviewed studies to analyze CH4 emissions calculated per unit of milk production, energy-corrected milk (ECM), average daily gain (ADG), dry matter intake (DMI), and gross energy intake (GEI), and related emissions to rumen fermentation profiles (volatile fatty acids [VFA], hydrogen [H2]) and microflora activities in the rumen of beef and dairy cattle. For dairy cattle, there was a positive correlation (p < 0.001) between CH4 emissions and DMI (R2 = 0.44), milk production (R2 = 0.37; p < 0.001), ECM (R2 = 0.46), GEI (R2 = 0.50), and acetate/propionate (A/P) ratio (R2 = 0.45). For beef cattle, CH4 emissions were positively correlated (p < 0.05−0.001) with DMI (R2 = 0.37) and GEI (R2 = 0.74). Additionally, the ADG (R2 = 0.19; p < 0.01) and A/P ratio (R2 = 0.15; p < 0.05) were significantly associated with CH4 emission in beef steers. This information may lead to cost-effective methods to reduce enteric CH4 production from cattle. We conclude that enteric CH4 emissions per unit of ECM, GEI, and ADG, as well as rumen fermentation profiles, show great potential for estimating enteric CH4 emissions.

Residual Feed Intake and Rumen Metabolism in Growing Pelibuey Sheep

This study was carried out to evaluate the residual feed intake (RFI), volatile fatty acid (VFA) production and enteric methane (CH4) from growing Pelibuey sheep. In this case, 12 non-castrated Pelibuey with an initial average live weight (LW) of 21.17 ± 3.87 kg and an age of 3 months, were housed in individual pens and fed a basal diet with 16% of crude protein and 11 MJ ME for 45 days. Dry matter intake (DMI) was measured and the daily weight gain (DWG) was calculated using a linear regression between the LW and experimental period. Mean metabolic live weight (LW0.75) was calculated. RFI was determined by linear regression with DWG and LW0.75 as independent variables. Lambs were classified as low, medium, and high RFI. Feed efficiency was determined as DWG/DMI. For determining rumen pH, ammonia nitrogen concentration NH3-N), and VFA, ruminal fluid was obtained using an esophageal probe on day 40. Feed intake of low RFI lambs was approximately 16% lower (p < 0.05) while growth rate was not significantly different. Their average energy loss, expressed as CH4 production per kilogram of metabolic weight, was 17% lower (p < 0.05).

A mathematical nutrition model adequately predicts beef and dairy cow intake and biological efficiency

The beef cow-calf sector accounts for 70% of feed consumed and greenhouse gases emitted for the beef industry, but there is no straightforward method to measure biological efficiency in grazing conditions. The objective of this study was to evaluate a mathematical nutrition model to estimate the feed intake and biological efficiency of mature beef cows. Data from dams (N = 160) and their second and third progeny (312 pairs) were collected from 1953 through 1980. Individual feed intake was measured at 28-d intervals year-round for dams and during 240-d lactation for progeny. Body weights of progeny were measured at 28-d intervals from birth to weaning, and of dams at parturition and weaning each production cycle. The milk yield of dams was measured at 14-d intervals. Dam metabolizable energy intake (DMEI) and milk energy yield (MEL) of each cow were predicted using the Cattle Value Discovery System beef cow (CVDSbc) model for each parity. Biological efficiency (Mcal/kg) was computed as the ratio of observed or predicted DMEI to observed calf weaning weight (PWW). Pearson correlation coefficients were computed using corr.test function and model evaluation was performed using the epiR function in R software. Average (SD) dam weight, PWW, DMEI, and observed MEL were 527 (86) kg, 291 (47) kg, 9584 (2701) Mcal/production cycle, and 1029 (529) Mcal, respectively. Observed and predicted DMEI (r = 0.93 and 0.91), and observed and predicted MEL (r = 0.58 and 0.59) were positively correlated for progeny 2 and 3, respectively. The CVDSbc model under-predicted DMEI (mean bias [MB] = 1,120 ± 76 Mcal, 11.7% of observed value) and MEL (MB = 30 ± 25 Mcal, 2.9% of observed value). Observed and predicted progeny feed intake were not correlated (r = 0.01, P-value = 0.79). Observed and predicted biological efficiency were positively correlated (r = 0.80 and 0.80, P-value ≤ 0.05) for parity 2 and 3, respectively, and the CVDSbc model under-predicted biological efficiency by 11% (MB = 3.59 ± 0.25 Mcal/kg). The CVDSbc provides reasonable predictions of feed intake and biological efficiency of mature beef cows, but further refinement of the relationship between calf feed intake and milk yield is recommended to improve predictions. Mathematical nutrition models can assist in the discovery of the biological efficiency of mature beef cows.

Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq

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The most active archaea in the epimural community were different from that of the liquid and content-associated community, but the exact taxonomy requires further identification.

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Rumen epithelial attached methanogens may not contribute to differences in CH₄ production and variations in feed efficiency.

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Families Campylobacteraceae and Neisseriaceae, which contain oxygen scavenging bacteria were significantly more active on the epithelium of efficient cattle.

To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

BACKGROUND

Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle.

RESULTS

Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10-5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules.

CONCLUSIONS

This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.

Phenotypic association among performance, feed efficiency and methane emission traits in Nellore cattle

Enteric methane (CH4) emissions are a natural process in ruminants and can result in up to 12% of energy losses. Hence, decreasing enteric CH4 production constitutes an important step towards improving the feed efficiency of Brazilian cattle herds. The aim of this study was to evaluate the relationship between performance, residual feed intake (RFI), and enteric CH4 emission in growing Nellore cattle (Bos indicus). Performance, RFI and CH4 emission data were obtained from 489 animals participating in selection programs (mid-test age and body weight: 414±159 days and 356±135 kg, respectively) that were evaluated in 12 performance tests carried out in individual pens (n = 95) or collective paddocks (n = 394) equipped with electronic feed bunks. The sulfur hexafluoride tracer gas technique was used to measure daily CH4 emissions. The following variables were estimated: CH4 emission rate (g/day), residual methane emission and emission expressed per mid-test body weight, metabolic body weight, dry matter intake (CH4/DMI), average daily gain, and ingested gross energy (CH4/GE). Animals classified as negative RFI (RFI<0), i.e., more efficient animals, consumed less dry matter (P <0.0001) and emitted less g CH4/day (P = 0.0022) than positive RFI animals (RFI>0). Nonetheless, more efficient animals emitted more CH4/DMI and CH4/GE (P < 0.0001), suggesting that the difference in daily intake between animals is a determinant factor for the difference in daily enteric CH4 emissions. In addition, animals classified as negative RFI emitted less CH4 per kg mid-test weight and metabolic weight (P = 0.0096 and P = 0.0033, respectively), i.e., most efficient animals could emit less CH4 per kg of carcass. In conclusion, more efficient animals produced less methane when expressed as g/day and per kg mid-test weight than less efficient animals, suggesting lower emissions per kg of carcass produced. However, it is not possible to state that feed efficiency has a direct effect on enteric CH4 emissions since emissions per kg of consumed dry matter and the percentage of gross energy lost as CH4 are higher for more efficient animals.

Review: Markers and proxies to monitor ruminal function and feed efficiency in young ruminants

Developing the rumen's capacity to utilise recalcitrant and low-value feed resources is important for ruminant production systems. Early-life nutrition and management practices have been shown to influence development of the rumen in young animals with long-term consequences on their performance. Therefore, there has been increasing interest to understand ruminal development and function in young ruminants to improve feed efficiency, health, welfare, and performance of both young and adult ruminants. However, due to the small size, rapid morphological changes and low initial microbial populations of the rumen, it is difficult to study ruminal function in young ruminants without major invasive approaches or slaughter studies. In this review, we discuss the usefulness of a range of proxies and markers to monitor ruminal function and nitrogen use efficiency (a major part of feed efficiency) in young ruminants. Breath sulphide and methane emissions showed the greatest potential as simple markers of a developing microbiota in young ruminants. However, there is only limited evidence for robust indicators of feed efficiency at this stage. The use of nitrogen isotopic discrimination based on plasma samples appeared to be the most promising proxy for feed efficiency in young ruminants. More research is needed to explore and refine potential proxies and markers to indicate ruminal function and feed efficiency in young ruminants, particularly for neonatal ruminants.

Relationships among feed efficiency traits across production segments and production cycles in cattle

Understanding the relationships between feed efficiency traits measured in different stages of production is necessary to improve feed efficiency across the beef value chain. The objective of this study was to evaluate relationships among feed efficiency traits measured as growing heifers and breeding females and in their progeny in three full production cycles, and relationships of dam residual feed intake (RFI) with lifetime and lifecycle cow efficiency traits. Data were collected on 160 mixed-breed heifers from 240 d of age to weaning of their third progeny, and postweaning performance of progeny until harvest in experiments initiated in 1953, 1954, 1959, 1964, 1969, and 1974. Individual feed offered was recorded daily, and feed refusals measured every 28 d. Milk yield was measured at 14-d intervals throughout lactation by machine or hand milking. Females and progeny were weighed at 28-d intervals and progeny were harvested at a constant endpoint of live grade or age depending upon the experiment. Feed efficiency traits of RFI and residual BW gain (RG) were computed as the residual from linear regression for developing heifers, dams (RFI and residual energy-corrected milk [RECM]), and postweaning progeny. Feed:gain ratio (FCR) was computed for developing heifers and postweaning progeny, and feed:milk energy ratio (FME) was computed for dams. Various measures of cow efficiency were calculated on either a life cycle or lifetime basis using ratios of progeny and dam weight outputs to progeny and dam feed inputs. Pearson correlations were computed among traits adjusted for a random year-breed-diet group effect. Heifer RFI (0.74) and RG (-0.32) were correlated (P ≤ 0.05) with dam RFI in parity 1 only, but were not correlated (P > 0.05) with dam RECM in any parity. Heifer RFI was correlated (P ≤ 0.05) with progeny RFI (0.17) in parity 3 only. Heifer FCR was not correlated with dam FME or progeny FCR in any parity. Dam RFI was weakly correlated (r = 0.25 to 0.36; P ≤ 0.05) among parities, whereas dam FME and RECM were strongly correlated (r = 0.49 to 0.72; P ≤ 0.05) among parities. Dam RFI in parity 1 and 2 was weakly correlated (r = -0.20 to -0.33; P ≤ 0.05) with cow efficiency ratios that included dam weight as an output, whereas dam RFI in parity 3 was not correlated with any cow efficiency ratio. In conclusion, feed efficiency traits were poorly correlated across production segments, but moderately repeatable across production cycles.

Breeding for reduced methane emission and feed-efficient Holstein cows: An international response

Selecting for lower methane (CH₄) emitting animals is one of the best approaches to reduce CH₄ given that genetic progress is permanent and cumulative over generations. As genetic selection requires a large number of animals with records and few countries actively record CH₄, combining data from different countries could help to expedite accurate genetic parameters for CH₄ traits and build a future genomic reference population. Additionally, if we want to include CH₄ in the breeding goal, it is important to know the genetic correlations of CH₄ traits with other economically important traits. Therefore, the aim of this study was first to estimate genetic parameters of 7 suggested methane traits, as well as genetic correlations between methane traits and production, maintenance, and efficiency traits using a multicountry database. The second aim was to estimate genetic correlations within parities and stages of lactation for CH₄. The third aim was to evaluate the expected response of economically important traits by including CH₄ traits in the breeding goal. A total of 15,320 methane production (MeP, g/d) records from 2,990 cows belonging to 4 countries (Canada, Australia, Switzerland, and Denmark) were analyzed. Records on dry matter intake (DMI), body weight (BW), body condition score, and milk yield (MY) were also available. Additional traits such as methane yield (MeY; g/kg DMI), methane intensity (MeI; g/kg energy-corrected milk), a genetic standardized methane production, and 3 definitions of residual methane production (g/d), residual feed intake, metabolic BW (MBW), BW change, and energy-corrected milk were calculated. The estimated heritability of MeP was 0.21, whereas heritability estimates for MeY and MeI were 0.30 and 0.38, and for the residual methane traits heritability ranged from 0.13 to 0.16. Genetic correlations between different methane traits were moderate to high (0.41 to 0.97). Genetic correlations between MeP and economically important traits ranged from 0.29 (MY) to 0.65 (BW and MBW), being 0.41 for DMI. Selection index calculations showed that residual methane had the most potential for inclusion in the breeding goal when compared with MeP, MeY, and MeI, as residual methane allows for selection of low methane emitting animals without compromising other economically important traits. Inclusion of residual feed intake in the breeding goal could further reduce methane, as the correlation with residual methane is moderate and elicits a favorable correlated response. Adding a negative economic value for methane could facilitate a substantial reduction in methane emissions while maintaining an increase in milk production.

Residual feed intake and related biochemical parameters in male Sahiwal calves

This study was conducted to evaluate the differences in efficiency of feed utilisation in Sahiwal calves with low and high residual feed intake (RFI) by comparing feed intake, nutrient digestibility, growth traits and blood biochemical parameters. Eighteen growing male Sahiwal calves (aged 12 months, average body weight 120.04 kg) were selected and fed individually total mixed ration as per their requirements for a period of 60 days. Fifty per cent of maize grains in concentrate mixture containing 33% maize grains were replaced by fresh potatoes (DM basis). Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid test metabolic body size, calves were assigned into low and high RFI groups. Residual feed intake (RFI) values were calculated for individual calves and the calves were divided into low (–0.20) and high (+0.18) RFI groups. Low RFI animals consumed less dry matter than the expected or predicted one indicating their more efficiency of feed utilization. The intakes of DM and CP were 4.95 and 6.47% lower in low RFI animals compared to high RFI animals while average daily gain was higher in low RFI group. The digestibility of DM, OM, CP, EE, total carbohydrates, NDF and ADF were similar in low and high RFI groups, however, nitrogen retention was higher in low RFI group. Values of alanine amino transferase (25.85 vs. 35.72 IU/L), aspartate amino transferase (80.33 vs. 100.57 IU/L), total protein (7.34 and 8.24 mg/dL), blood urea nitrogen (15.45 and 22.22 mg/dL) and creatinine (1.27 and 1.78 mg/dL) were higher for high RFI as compared to low RFI group. The concentration of growth hormone, insulin and IGF-1 were similar in both the groups. From present study, it could be concluded that low RFI animals were more efficient in feed conversion.

Feeding Forage Mixtures of Ryegrass (Lolium spp.) with Clover (Trifolium spp.) Supplemented with Local Feed Diets to Reduce Enteric Methane Emission Efficiency in Small-Scale Dairy Systems: A Simulated Study

Simple Summary

The present study simulated the effects of different dairy cow diets based on local feeding strategies on enteric methane (CH₄) emissions and surpluses of crude protein (CP) in small-scale dairy systems (SSDS). Our study evaluated five scenarios of supplementation (S): without supplementation (control diet), meaning no supplements were provided, only pasture (S1); pasture supplemented with 4.5 kg dry matter (DM)/cow/day of commercial concentrate (CC) (S2); supplemented with 200 g DM/kg per milk produced of CC (S3); supplemented with ground maize grains and wet distiller brewery grains (S4); and S4 plus maize silage (S5). In addition, two pasture managements (cut-and-carry versus grazing) and two varieties of legumes (red clover vs. white clover) were considered. The results suggest that methane emissions and large nitrogen surpluses in the diet are affected by the type of supplementation given to cows, in addition to the management and chemical composition of the pastures offered. In SSDS, it is possible to formulate diets with local inputs to reduce excess nutrients and dependence on external inputs, increasing feed efficiency and reducing costs (excess of CP in the diet) and CH₄ emissions.

Abstract

In cattle, greenhouse gas (GHG) emissions and nutrient balance are influenced by factors such as diet composition, intake, and digestibility. This study evaluated CH₄ emissions and surpluses of crude protein, using five simulated scenarios of supplementation in small-scale dairy systems (SSDS). In addition, two pasture managements (cut-and-carry versus grazing) and two varieties of legumes (red clover vs. white clover) were considered. The diets were tested considering similar milk yield and chemical composition; CH₄ emission was estimated using Tier-2 methodology from the Intergovernmental Panel on Climate Change (IPCC), and the data were analyzed in a completely randomized 5 × 2 × 2 factorial design. Differences (p < 0.05) were found in predicted CH₄ emissions per kg of milk produced (g kg⁻¹ FCM 3.5%). The lowest predicted CH₄ emissions were found for S3 and S4 as well as for pastures containing white clover. Lower dietary surpluses of CP (p < 0.05) were observed for the control diet (1320 g CP/d), followed by S5 (1793 g CP/d), compared with S2 (2175 g CP/d), as well as in cut-and-carry management with red clover. A significant correlation (p < 0.001) was observed between dry matter intake and CH₄ emissions (g⁻¹ and per kg of milk produced). It is concluded that the environmental impact of formulating diets from local inputs (S3 and S4) can be reduced by making them more efficient in terms of methane kg⁻¹ of milk in SSDS.

Methane and carbon dioxide emissions and grazed forage intake from pregnant beef heifers previously classified for residual feed intake under drylot conditions

The objectives of this study were to quantify the effect of post-weaning residual feed intake (RFI) on subsequent grazed forage intake, methane (CH4), and carbon dioxide (CO2) emissions. Beef heifers classified for RFI adjusted for off-test backfat (RFIfat; 55 high and 56 low) at 9 mo of age were monitored 7 mo later for CH4 and CO2 emissions using the GreenFeed Emissions Monitoring system. About 56 of these heifers were also monitored as high and low RFIfat groups using open-path Fourier-transform infrared spectroscopy (OP-FTIR). Heifers were dosed with 1 kg of C32-labelled pellets once daily for 15 d, with twice daily fecal sampling the last 8 d to determine individual grazed forage intake using the n-alkane method. Low RFIfat pregnant heifers consumed less forage (10.25 vs. 10.81 kg dry matter d−1; P < 0.001), and emitted less daily CH4 (238.7 vs. 250.7 g d−1; P = 0.009) and CO2 (7578 vs. 8041 g d−1; P < 0.001) compared with high RFIfat animals. Results from the OP-FTIR further confirmed that low RFIfat heifers emitted 6.3% less (g d−1; P = 0.006) CH4 compared with their high RFIfat cohorts. Thus, selection for low RFIfat will decrease daily CH4 and CO2 emissions from beef cattle.

Comparative analyses of enteric methane emissions, dry matter intake, and milk somatic cell count in different residual feed intake categories of dairy cows

This study compared the different residual feed intake (RFI) categories of lactating Holsteins with respect to methane (CH4) emissions, dry matter intake (DMI, kg), milk somatic cell count (SCC, 103∙mL−1), and β-hydroxybutyrate (BHB, mmol∙L−1). The RFI was calculated in 131 lactating Holstein cows that were then categorized into −RFI (RFI < 0) vs. +RFI (RFI > 0) and low- [RFI < −0.5 standard deviation (SD)] vs. high-RFI (RFI > 0.5 SD) groups. Milk traits were recorded in 131 cows, whereas CH4 and carbon dioxide were measured in 83. Comparisons of −RFI vs. +RFI and low- vs. high-RFI showed 7.9% (22.3 ± 0.40 vs. 24.2 ± 0.39) and 12.8% (21.1 ± 0.40 vs. 24.2 ± 0.45) decrease (P < 0.05) in DMI of −RFI and low-RFI groups, respectively. Similarly, −RFI and low-RFI cows had lower (P < 0.05) CH4 (g∙d−1) by 9.7% (343.5 ± 11.1 vs. 380.4 ± 10.9) and 15.5% (332.5 ± 12.9 vs. 393.5 ± 12.6), respectively. Milk yield was not different (P > 0.05) in −RFI vs. +RFI and low vs. high comparisons. The −RFI and low-RFI cows had lower (P < 0.05) SCC in −RFI vs. +RFI and low-RFI vs. high-RFI comparisons. The BHB was lower (P < 0.05) in low-RFI compared with the high-RFI group. Low-RFI dairy cows consumed less feed, emitted less CH4 (g∙d−1), and had lower milk SCC and BHB without differing in milk yield.

Effects of dry yeast supplementation on growth performance, rumen fermentation characteristics, slaughter performance and microbial communities in beef cattle

This study aimed to investigate the effects of active dry yeast (ADY) on growth performance, rumen microbial composition and carcass performance of beef cattle. Thirty-two finishing beef cattle (yak ♂ × cattle-yaks ♀), with an average body weight of 110 ± 12.85 kg, were randomly assigned to one of four treatments: the low plane of nutrition group (control), low plane of nutrition group + ADY 2 g/head daily (ADY2), low plane of nutrition group + ADY 4 g/head daily (ADY4) and the high plane of nutrition group (HPN). Supplementation of ADY increased average daily gain compared to the control group. The neutral detergent fiber and acid detergent fiber apparent digestibility in HPN group was greater than that in control group. The propionic acid concentration in the rumen in ADY2, ADY4, and HPN groups was greater than that in control group. The Simpson and Shannon indexes in control and HPN groups were higher than that in ADY4 group. At the phylum level, the relative abundance of Firmicutes in the HPN group was higher than that in ADY4 group. The relative abundance of Ruminococcaceae UCG-002 in ADY4 group was higher than that in control and HPN groups. In conclusion, supplementation ADY 4 g/head daily shift the rumen microbial composition of beef cattle fed low plane of nutrition to a more similar composition with cattle fed with HPN diet and produce the similar carcass weight with HPN diet.HighlightsThe ADY can improve the utilization of nitrogen and decrease the negative impact on the environment in beef cattle.Cattle fed low plane of nutrition diet supplemented with ADY 4 g/head daily increased growth performance.Supplementation ADY 4 g/head daily in low plane of nutrition diet might be produced comparable carcass weight to HPN diet.

Estimating the environmental impact of dairy cattle breeding programs through emission intensity

A recently developed methodological approach for determining the greenhouse gas emissions impact of national breeding programs was applied to measure the effects of current and future breeding goals on the emission intensity (EI) of the Canadian dairy industry. Emission intensity is the ratio of greenhouse gas outputted in comparison to the product generated. Traits under investigation affected EI by either decreasing the direct emissions yield (i.e. increasing feed performance), changing herd structure (i.e. prolonging herd life) or through the dilution effect of increased production (i.e. increasing fat yield). The intensity value (IV) of each trait, defined as the change in emissions' intensity per unit change in each trait, was calculated for each of the investigated traits. The IV trend of these traits was compared for the current and prospective selection index, as well as for a system with and without quota (the supply management policy designed to prevent overproduction). The overall EI of the average genetic merit Canadian dairy herd per breeding female was 5.07 kg CO₂eq/kg protein equivalent output. The annual reduction in EI due to the improvement of production traits was -0.027, -0.018 and -0.006 for fat, protein and milk other solids, respectively. The functional traits, herd life and mastitis resistance, had more modest effects (-0.008 and -0.001, respectively). These results are consistent with international studies that identified traits related to production, survival, health and fertility as having the largest impact on the environmental footprint of dairy cattle. Overall, the dairy industry is becoming more efficient by reducing its EI through selection of environmentally favorable traits, with a 1% annual reduction of EI in Canada.

Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes

MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.

Ozone Decreased Enteric Methane Production by 20% in an in vitro Rumen Fermentation System

Ozone (O₃) is volatile, highly oxidative, and has theoretical potential to reduce ruminant enteric methanogenesis by interactions between archaea and bacteria, and substrate and oxygen. The effects of O₃ on the rumen microbiota, fermentation parameters, and CH₄ emissions were studied through in vitro fermentation using a RUSITEC apparatus with O₃ dissolved in the salivary buffer. The substrate consisted of maize silage or grain concentrates, and the treatments were (1) control (no O₃) and (2) O₃ at 0.07 ± 0.022 mg/L in the buffer. A 4-day adaptation period followed by a 6-day experimental period was used for measuring gas production and composition, as well as fermentation characteristics, which included ruminal volatile fatty acids (VFA) and liquid- and solid-associated microbial communities. Ozone treatment decreased total gas production by 15.4%, most notably CH₄ production by 20.4%, and CH₄ gas concentration by 5.8%, without compromising dry matter digestibility (DMD) of either maize silage or grain concentrates. There were no significant effects of O₃ treatment on VFA production or pH. Ozone treatment reduced the relative abundance of methanogens, particularly Methanomicrobium. This study demonstrates the potential use of O₃ as a method to reduce ruminant enteric methanogenesis.

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed

The relationship between rumen microbiota and host feed efficiency phenotype, for genetically divergent beef cattle breeds is unclear. This is further exacerbated when different growth stages, chemically diverse diets and production systems are considered. Residual feed intake (RFI), a measure of feed efficiency, was calculated for individually fed Charolais (CH) and Holstein-Friesian (HF) steers during each of four 70-day (excluding adaptation) successive dietary phases: namely, high-concentrate, grass silage, fresh zero-grazed grass and high-concentrate again. Rumen fluid from the ten highest- (HRFI) and ten lowest-ranking (LRFI) animals for RFI, within breed, during each dietary phase was collected using a trans-oesophageal sampler and subjected to 16S rRNA amplicon sequencing and metabolic profiling. The datasets were analysed to identify microbial and rumen fermentation markers associated with RFI status. Age, dietary phase and breed were included in the statistical model. Within breed, for each dietary phase, mid-test metabolic weight and average daily gain did not differ (P > 0.05) between HRFI and LRFI steers; however, for the initial high-concentrate, grass silage, fresh grass herbage and final high-concentrate dietary phases, HRFI HF steers consumed 19, 23, 18 and 27% more (P < 0.001) than their LRFI counterparts. Corresponding percentages for CH HRFI compared to CH LRFI steers were 18, 23, 13 and 22%. Ten OTUs were associated with RFI (q < 0.05) independent of the other factors investigated. Of these Methanomassiliicoccaceae, Mogibacteriaceae and the genus p-75-a5 of Erysipelotrichaceae and were negatively associated (q < 0.05) with RFI. The results gave evidence that microbial species could potentially be an indicator of RFI in ruminants rather than broader microbiome metrics; however, further research is required to elucidate this association.

Grouping crossbred Holstein x Gyr heifers according to different feed efficiency indexes and its effects on energy and nitrogen partitioning, blood metabolic variables and gas exchanges

The objectives of this study were: i) to classify animals into groups of high and low feed efficiency (FE) using three FE indexes (Residual feed intake (RFI), Residual weight gain (RG) and Feed conversion efficiency (FCE)), and ii) to evaluate whether crossbreed Holstein x Gyr heifers divergent for FE indexes exhibit differences in nutrient intake and digestibility, energy partitioning, heat production, methane emissions, nitrogen partitioning and blood parameters. Thirty-five heifers were housed in a tie-stall, received ad libitum TMR (75:25, corn silage: concentrate) and were ranked and classified into high (HE) or low efficiency (LE) for RFI, RG and FCE. The number of animals for each HE group were 13 (< 0.5 standard deviation (SD) for RFI, 11 for RG and 11 for FCE (> 0.5 SD) and for the LE were 10 (> 0.5 SD) for RFI, 11 for RG and 12 for FCE (< 0.5 SD). Gas exchanges (O₂ consumption, CO₂ and CH₄ production) in open-circuit respiratory chambers and whole tract digestibility trial was performed. A completely randomized experimental design was used and the data were analyzed by ANOVA and correlation study. High efficiency animals for RFI produced less CO_2, consumed less O₂ and had lower heat production (HP). Methane production was positively correlated with RFI. High efficiency RG had higher O₂ consumption and CO₂ production in relation to LE-RG. High efficiency FCE had greater NFC digestibility, higher positive energy balance (EB) and excreted (11.4 g/d) less nitrogen in urine. High efficiency RG and FCE groups emitted less CH₄ per kg of weight gain than LE animals. Animals HE for RFI and FCE had lower β-hydroxybutyrate and higher glucose concentrations, respectively. The differences in intake, digestibility, energy and nitrogen partition, CH₄ emission, blood metabolic variables and heat production between the HE and LE groups varied according to the efficiency indexes adopted. The HP (kcal/d/BW^0.75) was lower for HE animals for RFI and FCE indexes.

Methane and carbon dioxide emissions from yearling beef heifers and mature cows classified for residual feed intake under drylot conditions

This study quantified methane (CH4) and carbon dioxide (CO2) production from beef heifers and cows classified for residual feed intake adjusted for off-test backfat thickness (RFIfat) and reared in drylot during cold winter temperatures. Individual performance, daily feed intake, and RFIfat were obtained for 1068 crossbred and purebred yearling heifers (eight trials) as well as 176 crossbred mature cows (six trials) during the winters of 2015–2017 at two locations. A portion of these heifers (147 high RFIfat; 167 low RFIfat) and cows (69 high RFIfat; 70 low RFIfat) was monitored for enteric CH4 and CO2 emissions using the GreenFeed Emissions Monitoring (GEM) system (C-Lock Inc., Rapid City, SD, USA). Low RFIfat cattle consumed less feed [heifers, 7.80 vs. 8.48 kg dry matter (DM) d−1; cows, 11.64 vs. 13.16 kg DM d−1] and emitted less daily CH4 (2.5% for heifers; 3.7% for cows) and CO2 (1.4% for heifers; 3.4% for cows) compared with high RFIfat cattle. However, low RFIfat heifers and cows had higher CH4 (6.2% for heifers; 9.9% for cows) and CO2 yield (7.3% for heifers; 9.8% for cows) per kilogram DM intake compared with their high RFIfat pen mates. The GEM system performed at air temperatures between +20 and −30 °C. Feed intake of heifers and mature cows was differently affected by ambient temperature reduction between +20 and −15 °C and similarly increased their feed intake at temperatures below −15 °C. In conclusion, low RFIfat animals emit less daily enteric CH4 and CO2, due mainly to lower feed consumption at equal body weight, gain, and fatness.

Dietary mitigation of enteric methane emissions from ruminants: A review of plant tannin mitigation options

Methane gas from livestock production activities is a significant source of greenhouse gas (GHG) emissions which have been shown to influence climate change. New technologies offer a potential to manipulate the rumen biome through genetic selection reducing CH4 production. Methane production may also be mitigated to varying degrees by various dietary intervention strategies. Strategies to reduce GHG emissions need to be developed which increase ruminant production efficiency whereas reducing production of CH4 from cattle, sheep, and goats. Methane emissions may be efficiently mitigated by manipulation of natural ruminal microbiota with various dietary interventions and animal production efficiency improved. Although some CH4 abatement strategies have shown efficacy in vivo, more research is required to make any of these approaches pertinent to modern animal production systems. The objective of this review is to explain how anti-methanogenic compounds (e.g., plant tannins) affect ruminal microbiota, reduce CH4 emission, and the effects on host responses. Thus, this review provides information relevant to understanding the impact of tannins on methanogenesis, which may provide a cost-effective means to reduce enteric CH4 production and the influence of ruminant animals on global GHG emissions.