Effect of divergence in phenotypic residual feed intake on methane emissions, ruminal fermentation, and apparent whole-tract digestibility of beef heifers across three contrasting diets

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.

Rumen fermentation parameters and papillae development in Simmental growing bulls with divergent residual feed intake

Residual feed intake (RFI), a widespread index used to measure animal feed efficiency, is influenced by various individual biological factors related to inter-animal variation that need to be assessed. Herein, 30 Simmental bulls, raised under the same farm conditions, were divided on the basis of RFI values into a high efficient group (HE, RFI =  - 1.18 ± 0.33 kg DM/d, n = 15) and a low efficient group (LE, RFI = 0.92 ± 0.35 kg DM/d, n = 15). Subsequently, bulls were slaughtered at an average BW of 734 ± 39.4 kg. Their ruminal fermentation traits were analysed immediately after slaughtering and after 24 h of in vitro incubation. Furthermore, ruminal micro-biota composition and ruminal papillae morphology were examined. The LE group exhibited a higher propionate concentration as a percentage of total volatile fatty acids (17.3 vs 16.1%, P = 0.04) in the rumen fluid collected during slaughtering, which was also confirmed after in vitro fermentation (16.6 vs 15.4% respectively for LE and HE, P = 0.01). This phenomenon resulted in a significant alteration in the acetate-to-propionate ratio (A:P) with higher values for the HE group, both after slaughter (4.01 vs 3.66, P = 0.02) and after in vitro incubation (3.78 vs 3.66, P = 0.02). Methane production was similar in both groups either as absolute production (227 vs 218 mL for HE and LE, respectively) or expressed as a percentage of total gas (approximately 22%). Even if significant differences (P < 0.20) in the relative abundance of some bacterial genera were observed for the two RFI groups, no significant variations were observed in the alpha (Shannon index) and beta (Bray-Curtis index) diversity. Considering the papillae morphology, the LE subjects have shown higher length values (6.26 vs 4.90 mm, P < 0.01) while HE subjects have demonstrated higher papillae density (46.4 vs 40.5 n/cm2, P = 0.02). Histo-morphometric analysis did not reveal appreciable modifications in the total papilla thickness, boundaries or surface between the experimental groups. In conclusion, our results contribute to efforts to analyse the factors affecting feed efficiency at the ruminal level. Propionate production, papillae morphology and a few bacterial genera certainly play a role in this regard, although not a decisive one.

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.

Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls

The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.

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.

Residual feed intake in peripartal dairy cows is associated with differences in milk fat yield, ruminal bacteria, biopolymer hydrolyzing enzymes, and circulating biomarkers of immunometabolism

Residual feed intake (RFI) measures feed efficiency independent of milk production level, and is typically calculated using data past peak lactation. In the current study, we retrospectively classified multiparous Holstein cows (n = 320) from 5 of our published studies into most feed-efficient (M-eff) or least feed-efficient (L-eff) groups using performance data collected during the peripartal period. Objectives were to assess differences in profiles of plasma biomarkers of immunometabolism, relative abundance of key ruminal bacteria, and activities of digestive enzymes in ruminal digesta between M-eff and L-eff cows. Individual data from cows with ad libitum access to a total mixed ration from d -28 to d +28 relative to calving were used. A linear regression model including dry matter intake (DMI), energy-corrected milk (ECM), changes in body weight (BW), and metabolic BW was used to classify cows based on RFI divergence into L-eff (n = 158) and M-eff (n = 162). Plasma collected from the coccygeal vessel at various times around parturition (L-eff = 60 cows; M-eff = 47 cows) was used for analyses of 30 biomarkers of immunometabolism. Ruminal digesta collected via esophageal tube (L-eff = 19 cows; M-eff = 29 cows) was used for DNA extraction and assessment of relative abundance (%) of 17 major bacteria using real-time PCR, as well as activity of cellulase, amylase, xylanase, and protease. The UNIVARIATE procedure of SAS 9.4 (SAS Institute Inc.) was used for analyses of RFI coefficients. The MIXED procedure of SAS was used for repeated measures analysis of performance, milk yield and composition, plasma immunometabolic biomarkers, ruminal bacteria, and enzyme activities. The M-eff cows consumed less DMI during the peripartal period compared with L-eff cows. In the larger cohort of cows, despite greater overall BW for M-eff cows especially in the prepartum (788 vs. 764 kg), no difference in body condition score was detected due to RFI or the interaction of RFI × time. Milk fat content (4.14 vs. 3.75 ± 0.06%) and milk fat yield (1.75 vs. 1.62 ± 0.04 kg) were greater in M-eff cows. Although cumulative ECM yield did not differ due to RFI (1,138 vs. 1,091 ± 21 kg), an RFI × time interaction due to greater ECM yield was found in M-eff cows. Among plasma biomarkers studied, concentrations of nonesterified fatty acids, β-hydroxybutyrate, bilirubin, ceruloplasmin, haptoglobin, myeloperoxidase, and reactive oxygen metabolites were overall greater, and glucose, paraoxonase, and IL-6 were lower in M-eff compared with L-eff cows. Among bacteria studied, abundance of Ruminobacter amylophilus and Prevotella ruminicola were more than 2-fold greater in M-eff cows. Despite lower ruminal activity of amylase in M-eff cows in the prepartum, regardless of RFI, we observed a marked linear increase after calving in amylase, cellulase, and xylanase activities. Protease activity did not differ due to RFI, time, or RFI × time. Despite greater concentrations of biomarkers reflective of negative energy balance and inflammation, higher feed efficiency measured as RFI in peripartal dairy cows might be associated with shifts in ruminal bacteria and amylase enzyme activity. Further studies could help address such factors, including the roles of the liver and the mammary gland.

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.

Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake

Background

Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.

Results

The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P < 0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P < 0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P < 0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P < 0.01), Methanobrevibacter ruminantium (P = 0.09) and methanogenesis functions (P = 0.04).

Conclusions

The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00170-3.

Associations of Wearable Sensor Measures With Feed Intake, Production Traits, Lactation, and Environmental Parameters Impacting Feed Efficiency in Dairy Cattle

Feed efficiency is an important trait to dairy production because of its impact on sustainability and profitability. Measuring individual cow feed intake on commercial farms would be unfeasibly costly at present. Thus, developing cheap and portable indicators of feed intake would be highly beneficial for genetic selection and precision feeding management tools. Given the growing use of automated sensors on dairy farms, the objective of this study was to determine the relationship between measurements recorded from multiple wearable sensors and feed intake. A total of three different wearable sensors were evaluated for their association with dry mater intake (DMI). The sensors measured activity (sensors = 3), rumination (sensors = 1), ear temperature (sensors = 1), rumen pH (sensors = 1) and rumen temperature (sensors = 1). A range of 56–340 cows with assorted sensors from 24 to 313 days in milk (DIM) were modeled to evaluate associations with DIM, parity, and contemporary group (CG; comprised of pen and study cohort). Models extending upon these variables included known energy sinks (i.e., milk production, milk fat/protein and metabolic body weight), to characterize the association of sensors measures and DMI. Statistically significant (i.e., P &lt; 0.05) regression coefficients for individual sensor measures with DMI ranged from 9.01E-07 to −3.45 kg DMI/day. When integrating all measures from a single sensor in a model, estimated regression coefficients ranged 8.83E-07 to −3.48 kg DMI/day. Significant associations were also identified for milk production traits, parity, DIM and CG. Associations tended to be highest for timepoints around the time of feeding and when multiple measurements within a sensor were integrated in a single model. The findings of this study indicate sensor measures are associated with feed intake and other energy sink traits and variables impacting feed efficiency. This information would be helpful to improve feed and feeding efficiency on commercial farms as proxy measurements for feed intake.

Evaluation of Ingestive Behavior, Ruminal and Blood Parameters, Performance, and Thermography as a Phenotypic Divergence Markers of Residual Feed Intake in Rearing Dairy Heifers

Simple Summary

The selection of highly efficient animals will support meeting the world’s future demand for products and food of animal origin. Thus, the identification of efficient animals and an understanding of the mechanisms inherent to this efficiency is fundamental for the progress of breeding systems. In the present study, we identify highly efficient animals for residual feed intake in dairy heifers. This animal category is unexplored in relation to this index. We utilized the classical parameters evaluated in cattle of different ages to carry out the study on these animals.

Abstract

The objectives of this study were: (1) to identify and rank phenotypically divergent animals for residual feed intake (RFI) regarding their efficiency (high: HE or low: LE); (2) to evaluate their relationships with ingestive behavior, ruminal and blood parameters, performance, and infrared thermography; and (3) to determine if such measurements can be used as feed efficiency markers in rearing dairy heifers. Thirty-eight heifers, 143 d ± 4 (Mean ± SD) of age and 108.7 kg ± 17.9 of body weight were used. The animals were fed with a total mixed ration during the 91 d of the trial. A phenotypic divergence of DMI for RFI was observed between −0.358 and 0.337 kg/d for HE and LE, respectively. Dry matter intake (DMI) was lower in the HE (2.5 kg DMI/d vs. 3.1 kg DMI/d), as was the number of visits to the feed bin with consumption (59 vs. 71). Feed intake was the best predictor of said divergence. Water intake and number of visits to the feed bin were presented moderate correlations with RFI. The ruminal fermentation variables, blood metabolites, blood hormones (such as the other ingestive behavior variables), and infrared thermography were not able to accurately predict HE or LE animals.

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.

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.

Association between residual feed intake, digestion, ingestive behavior, enteric methane emission and nitrogen metabolism in Nellore beef cattle

This study aimed to evaluate nutrient intake and digestibility, enteric methane emission and nitrogen utilization efficiency in Nellore cattle ranked by residual feed intake (RFI). Twenty-four Nellore bulls at 466 ± 24 days of age and with 352 ± 14.6 kg of body weight, classified as low and high RFI, were evaluated. Animals were kept in individual pens for three periods of 28 days and variables were measured. Data were analyzed as repeated measures over time, considering as fixed effects RFI class, period and RFI class x period interaction, and linear (co)variate of age. No significant differences in dry matter or nutrient intake were detected between RFI classes, but total digestible nutrients intake tended to be lower in low RFI animals, and apparent nutrient digestibility was higher in high RFI animals. Partial efficiency of growth tended to be lower in high RFI animals. RFI class did not interfere with enteric methane production or microbial protein synthesis, but fecal nitrogen output was higher in low RFI animals. The greater efficiency of low RFI animals is consequence of lower maintenance requirements, since energy from higher nutrients digestibility in high RFI animals was spent on metabolic processes other than body tissue deposition.

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.

Review: Comparative methane production in mammalian herbivores

Methane (CH4) production is a ubiquitous, apparently unavoidable side effect of fermentative fibre digestion by symbiotic microbiota in mammalian herbivores. Here, a data compilation is presented of in vivo CH4 measurements in individuals of 37 mammalian herbivore species fed forage-only diets, from the literature and from hitherto unpublished measurements. In contrast to previous claims, absolute CH4 emissions scaled linearly to DM intake, and CH4 yields (per DM or gross energy intake) did not vary significantly with body mass. CH4 physiology hence cannot be construed to represent an intrinsic ruminant or herbivore body size limitation. The dataset does not support traditional dichotomies of CH4 emission intensity between ruminants and nonruminants, or between foregut and hindgut fermenters. Several rodent hindgut fermenters and nonruminant foregut fermenters emit CH4 of a magnitude as high as ruminants of similar size, intake level, digesta retention or gut capacity. By contrast, equids, macropods (kangaroos) and rabbits produce few CH4 and have low CH4 : CO2 ratios for their size, intake level, digesta retention or gut capacity, ruling out these factors as explanation for interspecific variation. These findings lead to the conclusion that still unidentified host-specific factors other than digesta retention characteristics, or the presence of rumination or a foregut, influence CH4 production. Measurements of CH4 yield per digested fibre indicate that the amount of CH4 produced during fibre digestion varies not only across but also within species, possibly pointing towards variation in microbiota functionality. Recent findings on the genetic control of microbiome composition, including methanogens, raise the question about the benefits methanogens provide for many (but apparently not to the same extent for all) species, which possibly prevented the evolution of the hosting of low-methanogenic microbiota across mammals.

Precision feed restriction improves feed and milk efficiencies and reduces methane emissions of less efficient lactating Holstein cows without impairing their performance

A possible driver of feed inefficiency in dairy cows is overconsumption. The objective was therefore to test precision feed restriction as a lever to improve feed efficiency of the least efficient lactating dairy cows. An initial cohort of 68 Holstein lactating cows was monitored from calving to end of ad libitum feeding at 196 ± 16 d in milk, with the last 70 d being used to estimate feed efficiency. For a given expected dry matter (DM) intake (DMI) during ad libitum feeding, offered DMI during restriction was set to observed DMI of the 10% most efficient cows during ad libitum feeding for similar performance. Feed restriction lasted during 92 d, with only the last 70 d being used for data analyses. A single diet was fed during ad libitum and restriction periods, and was based on 64.9% of corn silage and 35.1% of concentrates on a DM basis. Individual DMI, body weight, milk production, milk composition, and body condition score were recorded, as well as methane emissions. Feed efficiency was defined as the repeatable part of the random effect of cow on the intercept in a mixed model predicting DMI with net energy in milk, maintenance and body weight gain and loss within parity, feeding level, and time. Milk energy efficiency was estimated in the same way, predicting net energy in milk instead of DMI. The 15 least efficient cows ate 2.6 kg of DM/d more than the 15 most efficient cows during ad libitum feeding with 2 g/kg of DMI lower methane yield, but similar daily methane emissions. Feed restriction decreased DMI by 2.6 kg of DMI/d for the least efficient cows, which was 1.8 kg of DMI/d more than the most efficient cows, and decreased daily methane emissions by 49.2 g/d for the least efficient cows, which was 22.4 g/d more than the most efficient cows. Feed restriction had no significant effect on milk, body weight, or body weight change. Feed restriction reduced the variability of both milk energy and feed efficiencies, as shown by a decrease of their standard deviation from 0.87 to 0.69 kg of DM/d for feed efficiency and from 1.14 to 0.65 UFL/d for milk energy efficiency. Despite narrow efficiency differences, the most efficient cows during ad libitum feeding remained more efficient during feed restriction (r = 0.46 for feed efficiency and 0.49 for milk energy efficiency). The 2 efficiency groups no longer differed in feed efficiency during precision feed restriction. Precision feed restriction seemed to bring the least efficient cows closer to the most efficient cows and to reduce their methane emissions without impairing their performance.

Residual feed intake divergence during the preweaning period is associated with unique hindgut microbiome and metabolome profiles in neonatal Holstein heifer calves

BACKGROUND

Recent studies underscored that divergence in residual feed intake (RFI) in mature beef and dairy cattle is associated with changes in ruminal microbiome and metabolome profiles which may contribute, at least in part, to better feed efficiency. Because the rumen in neonatal calves during the preweaning period is underdeveloped until close to weaning, they rely on hindgut microbial fermentation to breakdown undigested diet components. This leads to production of key metabolites such as volatile fatty acids (VFA), amino acids, and vitamins that could potentially be absorbed in the hind-gut and help drive growth and development. Whether RFI divergence in neonatal calves is associated with changes in hindgut microbial communities and metabolites is largely unknown. Therefore, the objective of the current study was to determine differences in hindgut microbiome and metabolome in neonatal Holstein heifer calves retrospectively-grouped based on feed efficiency as most-efficient (M-eff) or least-efficient (L-eff) calves using RFI divergence during the preweaning period.

METHODS

Twenty-six Holstein heifer calves received 3.8 L of first-milking colostrum from their respective dams within 6 h after birth. Calves were housed in individual outdoor hutches bedded with straw, fed twice daily with a milk replacer, and had ad libitum access to a starter grain mix from birth to weaning at 42 d of age. Calves were classified into M-eff [n = 13; RFI coefficient = - 5.72 ± 0.94 kg DMI (milk replacer + starter grain)/d] and L-eff [n = 13; RFI coefficient = 5.61 ± 0.94 kg DMI (milk replacer + starter grain)/d] based on a linear regression model including the combined starter grain mix and milk replacer DMI, average daily gain (ADG), and metabolic body weight (MBW). A deep sterile rectal swab exposed only to the rectum was collected immediately at birth before colostrum feeding (i.e., d 0), and fecal samples at d 14, 28, and 42 (prior to weaning) for microbiome and untargeted metabolome analyses using 16S rRNA gene sequencing and LC-MS. Microbiome data were analyzed with the QIIME 2 platform and metabolome data with the MetaboAnalyst 4.0 pipeline.

RESULTS

No differences (P > 0.05) in body measurements including body weight (BW), body length (BL), hip height (HH), hip width (HW), and wither height (WH) were detected between M-eff and L-eff calves at birth and during preweaning. Although milk replacer intake did not differ between groups, compared with L-eff, M-eff heifers had lower starter intake (P < 0.01) between d 18 to 42 of age, whereas no differences (P > 0.05) for ADG, cumulative BWG, or body measurements were observed between RFI groups during the preweaning period. Microbiome and metabolome profiles through the first 42 d of age indicated greater hindgut capacity for the production of energy-generating substrates (butyrate and propionate) and essential nutrients (vitamins and amino acids) in heifers with greater estimated feed efficiency.

CONCLUSION

Despite consuming approximately 54.6% less solid feed (cumulative intake, 10.90 vs. 19.98 ± 1.66 kg) from birth to weaning, the microbiome-metabolome changes in the hindgut of most-efficient heifers might have helped them maintain the same level of growth as the least-efficient heifers.

Methane and Carbon Dioxide Emission of Beef Heifers in Relation with Growth and Feed Efficiency

Simple Summary

For sustainable meat production, beef farmers must make the best use of grass and roughage while limiting the carbon footprint of their herds. The genetic improvement in feed efficiency and enteric methane production of replacement heifers is possible if the recorded phenotypes are available. Intuitively, the relationship between the two traits should be negative, i.e., favorable, since the energy lost with the methane is not available for heifer metabolism. The measurement of feed efficiency requires several weeks of feed intake recording. The enteric methane emission rate can also be recorded over several weeks. The two traits of 326 beef heifers from two experimental farms were measured simultaneously for 8 to 12 weeks. The correlations between roughage intake, daily gain, and methane were all positive. The enteric methane emission rate was positively related to body weight, daily gain, and dry matter intake. The relationship with feed efficiency was slightly positive, i.e., unfavorable. Therefore, the two traits should be recorded simultaneously to evidence low-emitting and efficient heifers. This study also showed that replacing the feed intake recording with the carbon dioxide emission rate appeared potentially beneficial for selecting these low-emitting and efficient heifers.

Abstract

Reducing enteric methane production and improving the feed efficiency of heifers on roughage diets are important selection objectives for sustainable beef production. The objective of the current study was to assess the relationship between different methane production and feed efficiency criteria of beef heifers fed ad libitum roughage diets. A total of 326 Charolais heifers aged 22 months were controlled in two farms and fed either a grass silage (n = 252) or a natural meadow hay (n = 74) diet. Methane (CH₄) and carbon dioxide (CO₂) emission rates (g/day) were measured with GreenFeed systems. The dry matter intake (DMI), average daily gain (ADG), CH₄ and CO₂ were measured over 8 to 12 weeks. Positive correlations were observed among body weight, DMI, ADG, CH₄ and CO₂. The residual feed intake (r_wgDMI) was not related to CH₄ or residual methane (r_wiCH₄). It was negatively correlated with methane yield (CH₄/DMI): R_p = −0.87 and −0.83. Residual gain (r_wiADG) and ADG/DMI were weakly and positively related to residual methane (r_wiCH₄): R_p = 0.21 on average. The ratio ADG/CO₂ appeared to be a useful proxy of ADG/DMI (R_p = 0.64 and 0.97) and CH₄/CO₂ a proxy of methane yield (R_p = 0.24 and 0.33) for selecting low-emitting and efficient heifers.

Associations between residual feed intake and apparent nutrient digestibility, in vitro methane-producing activity, and volatile fatty acid concentrations in growing beef cattle1

The objectives of this study were to examine the relationship between residual feed intake (RFI) and DM and nutrient digestibility, in vitro methane production, and volatile fatty acid (VFA) concentrations in growing beef cattle. Residual feed intake was measured in growing Santa Gertrudis steers (Study 1; n = 57; initial BW = 291.1 ± 33.8 kg) and Brangus heifers (Study 2; n = 468; initial BW = 271.4 ± 26.1 kg) fed a high-roughage-based diet (ME = 2.1 Mcal/kg DM) for 70 d in a Calan-gate feeding barn. Animals were ranked by RFI based on performance and feed intake measured from day 0 to 70 (Study 1) or day 56 (Study 2) of the trial, and 20 animals with the lowest and highest RFI were identified for subsequent collections of fecal and feed refusal samples for DM and nutrient digestibility analysis. In Study 2, rumen fluid and feces were collected for in vitro methane-producing activity (MPA) and VFA analysis in trials 2, 3, and 4. Residual feed intake classification did not affect BW or BW gain (P > 0.05), but low-RFI steers and heifers both consumed 19% less (P < 0.01) DMI compared with high-RFI animals. Steers with low RFI tended (P < 0.1) to have higher DM digestibility (DMD) compared with high-RFI steers (70.3 vs. 66.5 ± 1.6% DM). Heifers with low RFI had 4% higher DMD (76.3 vs. 73.3 ± 1.0% DM) and 4 to 5% higher (P < 0.01) CP, NDF, and ADF digestibility compared with heifers with high RFI. Low-RFI heifers emitted 14% less (P < 0.01) methane (% GE intake; GEI) calculated according to Blaxter and Clapperton (1965) as modified by Wilkerson et al. (1995), and tended (P = 0.09) to have a higher rumen acetate:propionate ratio than heifers with high RFI (GEI = 5.58 vs. 6.51 ± 0.08%; A:P ratio = 5.02 vs. 4.82 ± 0.14%). Stepwise regression analysis revealed that apparent nutrient digestibilities (DMD and NDF digestibility) for Study 1 and Study 2 accounted for an additional 8 and 6%, respectively, of the variation in intake unaccounted for by ADG and mid-test BW0.75. When DMD, NDF digestibility, and total ruminal VFA were added to the base model for Study 2, trials 2, 3, and 4, the R2 increased from 0.33 to 0.47, explaining an additional 15% of the variation in DMI unrelated to growth and body size. On the basis of the results of these studies, differences in observed phenotypic RFI in growing beef animals may be a result of inter-animal variation in apparent nutrient digestibility and ruminal VFA concentrations.

Digestibility contributes to between-animal variation in feed efficiency in beef cows

Residual feed intake (RFI) is an alternative measure of feed efficiency (FE) and is calculated as the difference between actual and expected feed intake. The biological mechanisms underlying animal-to-animal variation in FE are not well understood. The aim of this study was to investigate the digestive ability of beef cows selected for RFI divergence as heifers, using two contrasted diets. Fifteen 4-year-old beef cows were selected from a total of 69 heifers based on their RFI following the feedlot test. The selected heifers were ranked into high-RFI (+ 1.02 ± 0.28, n = 8) and low-RFI (-0.73 ± 0.28, n = 7), and a digestibility trial was performed after their first lactation. Both RFI groups were offered two different diets: 100% hay or a fattening diet which consisted of a DM basis of 67% whole-plant maize silage and 33% high starch concentrates over four experimental periods (two per diet). A diet effect was observed on feed intake and apparent digestibility, whereas no diet × RFI interaction was detected (P > 0.05). Intake and apparent digestibility were higher in cows fed the fattening diet than in those fed the hay diet (P < 0.0001). DM intake (DMI) and organic matter apparent digestibility (OMd) were repeatable and positively correlated between the two subsequent periods of measurements. For the hay and fattening diets, the repeatability between periods was r = 0.71 and r = 0.73 for DMI and r = 0.87 and r = 0.48 for OMd, respectively. Moreover, both intake (r = 0.55) and OMd (r = 0.54) were positively correlated (P < 0.05) between the hay and fattening diets. Significant differences between beef cows selected for divergence in RFI as heifers were observed for digestive traits (P < 0.05), DM and organic matter (OM) apparent digestibility being higher for low-RFI cows. Overall, this study showed that apparent digestibility contributes to between-animal variation in FE in beef cows.

Hot topic: Selecting cattle for low residual feed intake did not affect daily methane production but increased methane yield

Reducing enteric methane (CH₄) production and improving feed conversion efficiency of dairy cows is of high importance. Residual feed intake (RFI) is one measure of feed efficiency, with low RFI animals being more efficient in feed conversion. Enteric CH₄ is an important source of digestible energy loss in ruminants and, because research in beef cattle has reported a positive relationship between RFI and daily CH₄ production, we hypothesized that low RFI dairy heifers, which are more feed efficient, would produce less CH₄/d. We measured the daily methane production (g of CH₄/d), methane yield [g of CH₄/kg of dry matter intake (DMI)], and CH₄ per kilogram of body weight (BW) gain for 56 heifers (20-22 mo old) in a 2 × 2 factorial arrangement: factors included 2 breeds (Holstein-Friesian and Jersey; n = 28/breed), with equal numbers of animals previously determined as being either high [+2.0 kg of dry matter (DM)/d] or low RFI (-2.1 kg of DM/d; n = 28/RFI category). All heifers were commingled and offered unrestricted access to the same diet of dried alfalfa cubes. Between RFI categories, heifers did not differ in BW or BW gain but low RFI heifers had 9.3 and 10.6% lower DMI and DMI/kg of BW, respectively, than high RFI heifers. Similarly, RFI category did not affect CH₄/d or CH₄/kg of BWg, but CH₄/kg of DMI was higher in low RFI heifers because of their lower DMI. These results might reflect more complete digestion of ingested feed in the more efficient, low RFI heifers, consistent with previous reports of greater apparent digestibility of organic matter. Holstein-Friesian heifers were heavier and consumed more total DM than Jersey heifers, but breed did not affect DMI/kg of BW or BWg. Jersey heifers produced less CH₄/d, but not CH₄/kg of DMI or CH₄/kg of BWg. We detected no interaction between breed and RFI category in any of the variables measured. In conclusion, differences in RFI in dairy heifers did not affect daily CH₄ production (g/d); however, low RFI heifers had a greater CH₄ yield (g/kg of DMI) on a high forage diet.

Residual feed intake in beef cattle and its association with carcass traits, ruminal solid-fraction bacteria, and epithelium gene expression

Background

Residual feed intake (RFI) describes an animal’s feed efficiency independent of growth performance. The objective of this study was to determine differences in growth performance, carcass traits, major bacteria attached to ruminal solids-fraction, and ruminal epithelium gene expression between the most-efficient and the least-efficient beef cattle. One-hundred and forty-nine Red Angus cattle were allocated to three contemporary groups according to sex and herd origin. Animals were fed a finishing diet in confinement for 70 d to determine the RFI category for each. Within each group, the two most-efficient (n = 6; RFI coefficient = − 2.69 ± 0.58 kg dry matter intake (DMI)/d) and the two least-efficient animals (n = 6; RFI coefficient = 3.08 ± 0.55 kg DMI/d) were selected. Immediately after slaughter, ruminal solids-fraction and ruminal epithelium were collected for bacteria relative abundance and epithelial gene expression analyses, respectively, using real-time PCR.

Results

The most-efficient animals consumed less feed (P = 0.01; 5.03 kg less DMI/d) compared with the least-efficient animals. No differences (P > 0.10) in initial body weight (BW), final BW, and average daily gain (ADG) were observed between the two RFI classes. There were no significant RFI × sex effects (P > 0.10) on growth performance. Compared with the least-efficient group, hot carcass weight (HCW), ribeye area (REA), and kidney, pelvic, and heart fat (KPH) were greater (P ≤ 0.05) in the most-efficient cattle. No RFI × sex effect (P > 0.10) for carcass traits was detected between RFI groups. Of the 10 bacterial species evaluated, the most-efficient compared with least efficient cattle had greater (P ≤ 0.05) relative abundance of Eubacterium ruminantium, Fibrobacter succinogenes, and Megasphaera elsdenii, and lower (P ≤ 0.05) Succinimonas amylolytica and total bacterial density. No RFI × sex effect on ruminal bacteria was detected between RFI groups. Of the 34 genes evaluated in ruminal epithelium, the most-efficient cattle had greater (P ≤ 0.05) abundance of genes involved in VFA absorption, metabolism, ketogenesis, and immune/inflammation-response. The RFI × sex interactions indicated that responses in gene expression between RFI groups were due to differences in sex. Steers in the most-efficient compared with least-efficient group had greater (P ≤ 0.05) expression of SLC9A1, HIF1A, and ACO2. The most-efficient compared with least-efficient heifers had greater (P ≤ 0.05) mRNA expression of BDH1 and lower expression (P ≤ 0.05) of SLC9A2 and PDHA1.

Conclusions

The present study revealed that greater feed efficiency in beef cattle is associated with differences in bacterial species and transcriptional adaptations in the ruminal epithelium that might enhance nutrient delivery and utilization by tissues. The lack of RFI × sex interaction for growth performance and carcass traits indicates that sex may not play a major role in improving these phenotypes in superior RFI beef cattle. However, it is important to note that this result should not be considered a solid biomarker of efficient beef cattle prior to further examination due to the limited number of heifers compared with steers used in the study.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0283-8) contains supplementary material, which is available to authorized users.

16S rRNA Sequencing Reveals Relationship Between Potent Cellulolytic Genera and Feed Efficiency in the Rumen of Bulls

The rumen microbial population dictates the host’s feed degradation capacity and subsequent nutrient supply. The rising global human population and intensifying demand for animal protein is creating environmental challenges. As a consequence, there is an increasing requirement for livestock with enhanced nutrient utilization capacity in order to more efficiently convert plant material to high quality edible muscle. In the current study, residual feed intake (RFI), a widely used and a highly accepted measure of feed efficiency in cattle, was calculated for a combination of three cohorts of Simmental bulls. All animals were managed similarly from birth and offered concentrate ad libitum in addition to 3 kg of grass silage daily during the finishing period. Solid and liquid rumen digesta samples collected at slaughter and were analyzed using amplicon sequencing targeting the 16S rRNA gene utilizing the Illumina MiSeq platform. Volatile fatty acid analysis was also conducted on the liquid digesta samples. Spearman’s correlation coefficient was utilized to determine the association between RFI and bacterial and archaeal taxa and inter-taxonomic relationships. The data indicate a tendency toward an increase in butyrate (P = 0.06), which corresponds with an increase in plasma β-hydroxybutyrate concentration in low RFI (LRFI) bulls in comparison to their high RFI (HRFI) contemporaries (P < 0.05). A decrease in propionate (P < 0.05) was also recorded in the rumen of LRFI in comparison to HRFI bulls. These results indicate alternate fermentation patterns in the rumen of LRFI bulls. The data also identified that OTUs within the phyla Tenericutes, Fibrobacteres, and Cyanobacteria may potentially influence RFI phenotype. In particular, a negative association between F. succinogenes and RFI was evident. The unique cellulolytic metabolism of F. succinogenes suggests it could contribute to host efficiency by providing substrate to the host ruminant and other microbial populations (e.g., Selenomonas ruminantium, Methanobrevibacter, and Methanomassiliicoccaceae) in the rumen. This study provides evidence that bacterial OTUs within common phyla could influence ruminant feed efficiency phenotype through their role in ruminal degradation of complex plant polysaccharides or increased capability to harvest nutrients from ingested feed.

Association of residual feed intake with abundance of ruminal bacteria and biopolymer hydrolyzing enzyme activities during the peripartal period and early lactation in Holstein dairy cows

Background

Residual feed intake (RFI) in dairy cattle typically calculated at peak lactation is a measure of feed efficiency independent of milk production level. The objective of this study was to evaluate differences in ruminal bacteria, biopolymer hydrolyzing enzyme activities, and overall performance between the most- and the least-efficient dairy cows during the peripartal period. Twenty multiparous Holstein dairy cows with daily ad libitum access to a total mixed ration from d − 10 to d 60 relative to the calving date were used. Cows were classified into most-efficient (i.e. with low RFI, n = 10) and least-efficient (i.e. with high RFI, n = 10) based on a linear regression model involving dry matter intake (DMI), fat-corrected milk (FCM), changes in body weight (BW), and metabolic BW.

Results

The most-efficient cows had ~ 2.6 kg/d lower DMI at wk 4, 6, 7, and 8 compared with the least-efficient cows. In addition, the most-efficient cows had greater relative abundance of total ruminal bacterial community during the peripartal period. Compared with the least-efficient cows, the most-efficient cows had 4-fold greater relative abundance of Succinivibrio dextrinosolvens at d − 10 and d 10 around parturition and tended to have greater abundance of Fibrobacter succinogenes and Megaspheara elsdenii. In contrast, the relative abundance of Butyrivibrio proteoclasticus and Streptococcus bovis was lower and Succinimonas amylolytica and Prevotella bryantii tended to be lower in the most-efficient cows around calving. During the peripartal period, the most-efficient cows had lower enzymatic activities of cellulase, amylase, and protease compared with the least-efficient cows.

Conclusions

The results suggest that shifts in ruminal bacteria and digestive enzyme activities during the peripartal period could, at least in part, be part of the mechanism associated with better feed efficiency in dairy cows.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0258-9) contains supplementary material, which is available to authorized users.

Enteric methane emissions from low- and high-residual feed intake beef heifers measured using GreenFeed and respiration chamber techniques

The objectives of this study were to evaluate the relationship between residual feed intake (RFI; g/d) and enteric methane (CH) production (g/kg DM) and to compare CH and carbon dioxide (CO) emissions measured using respiration chambers (RC) and the GreenFeed emission monitoring (GEM) system (C-Lock Inc., Rapid City, SD). A total of 98 crossbred replacement heifers were group housed in 2 pens and fed barley silage ad libitum and their individual feed intakes were recorded by 16 automated feeding bunks (GrowSafe, Airdrie, AB, Canada) for a period of 72 d to determine their phenotypic RFI. Heifers were ranked on the basis of phenotypic RFI, and 16 heifers (8 with low RFI and 8 with high RFI) were randomly selected for enteric CH and CO emissions measurement. Enteric CH and CO emissions of individual animals were measured over two 25-d periods using RC (2 d/period) and GEM systems (all days when not in chambers). During gas measurements metabolic BW tended to be greater ( ≤ 0.09) for high-RFI heifers but ADG tended ( = 0.09) to be greater for low-RFI heifers. As expected, high-RFI heifers consumed 6.9% more feed ( = 0.03) compared to their more efficient counterparts (7.1 vs. 6.6 kg DM/d). Average CH emissions were 202 and 222 g/d ( = 0.02) with the GEM system and 156 and 164 g/d ( = 0.40) with RC for the low- and high-RFI heifers, respectively. When adjusted for feed intake, CH yield (g/kg DMI) was similar for high- and low-RFI heifers (GEM: 27.7 and 28.5, = 0.25; RC: 26.5 and 26.5, = 0.99). However, CH yield differed between the 2 measurement techniques only for the high-RFI group ( = 0.01). Estimates of CO yield (g/kg DMI) also differed between the 2 techniques ( ≤ 0.03). Our study found that high- and low-efficiency cattle produce similar CH yield but different daily CH emissions. The 2 measurement techniques differ in estimating CH and CO emissions, partially because of differences in conditions (lower feed intakes of cattle while in chambers, fewer days measured in chambers) during measurement. We conclude that when intake of animals is known, the GEM system offers a robust and accurate means of estimating CH emissions from animals under field conditions.

Associations of rumen parameters with feed efficiency and sampling routine in beef cattle

Characterizing ruminal parameters in the context of sampling routine and feed efficiency is fundamental to understand the efficiency of feed utilization in the bovine. Therefore, we evaluated microbial and volatile fatty acid (VFA) profiles, rumen papillae epithelial and stratum corneum thickness and rumen pH (RpH) and temperature (RT) in feedlot cattle. In all, 48 cattle (32 steers plus 16 bulls), fed a high moisture corn and haylage-based ration, underwent a productive performance test to determine residual feed intake (RFI) using feed intake, growth, BW and composition traits. Rumen fluid was collected, then RpH and RT logger were inserted 5.5±1 days before slaughter. At slaughter, the logger was recovered and rumen fluid and rumen tissue were sampled. The relative daily time spent in specific RpH and RT ranges were determined. Polynomial regression analysis was used to characterize RpH and RT circadian patterns. Animals were divided into efficient and inefficient groups based on RFI to compare productive performance and ruminal parameters. Efficient animals consumed 1.8 kg/day less dry matter than inefficient cattle (P⩽0.05) while achieving the same productive performance (P⩾0.10). Ruminal bacteria population was higher (P⩽0.05) (7.6×1011 v. 4.3×1011 copy number of 16S rRNA gene/ml rumen fluid) and methanogen population was lower (P⩽0.05) (2.3×109 v. 4.9×109 copy number of 16S rRNA gene/ml rumen fluid) in efficient compared with inefficient cattle at slaughter with no differences (P⩾0.10) between samples collected on-farm. No differences (P⩾0.10) in rumen fluid VFA were also observed between feed efficiency groups either on-farm or at slaughter. However, increased (P⩽0.05) acetate, and decreased (P⩽0.05) propionate, butyrate, valerate and caproate concentrations were observed at slaughter compared with on-farm. Efficient had increased (P⩽0.05) rumen epithelium thickness (136 v. 126 µm) compared with inefficient cattle. Efficient animals also spent 318% and 93.2% more time (P⩽0.05) in acidotic (4.14% v. 1.30%) (pH⩽5.6) and optimal (5.6<pH<6.0) (8.53% v. 4.42%) RpH range compared with inefficient cattle. The circadian patterns revealed lower (P⩽0.05) RpH and no differences (P⩾0.10) in RT pre-, during, and post-prandial periods in efficient compared with inefficient cattle. In essence, superior feed efficiency in cattle seems linked to rumen features consistent with improved efficiency of feed utilization. Microbial abundance, rumen epithelial histomorphology, and RpH, may serve as indicators for feed efficiency in cattle. The divergences of assessments made on-farm and at slaughter should be considered in the development of proxies for feed efficiency.

Growth performance, rumen fermentation, bacteria composition, and gene expressions involved in intracellular pH regulation of rumen epithelium in finishing Hu lambs differing in residual feed intake phenotype

The objective of this study was to evaluate the effect of residual feed intake (RFI) on rumen function in finishing lambs. A total of 60 male Hu lambs (average initial BW = 25.2 ± 2.5kg) were used and were offered a pelleted high-concentrate diet, of which the forage to concentrate ratio was 25:75. Individual feed intake was recorded over a period of 42 d, then 10 lambs with the lowest RFI and the highest RFI were selected, respectively. The rumen fluid used for fermentation variables and relative abundance of bacteria measurement was obtained on d 10 and 20 after RFI measurement. At the end of this experiment, the selected lambs were slaughtered and rumen epithelium and liver tissues were collected for RNA extraction. Low-RFI lambs had lower ( < 0.01) DMI and greater ( < 0.05) G:F than the high-RFI ones, while the RFI groups did not differ in ADG and BW ( > 0.05). Additionally, RFI was positively ( = 0.57; < 0.01) correlated with DMI and negatively ( = -0.53; < 0.05) correlated with G:F. Total VFA and individual VFA decreased ( < 0.05) over time. The concentrations of total VFA, acetate, valerate, isobutyrate, isovalerate, and rumen pH ( > 0.05) were not affected by RFI classification. Nonetheless, low-RFI group lambs had a greater ( < 0.05) concentration of propionate, a lower ( < 0.05) concentration of butyrate, and a lower ( < 0.05) acetate to propionate ratio compared with the high-RFI group. There was a significant ( < 0.05) effect of RFI on the relative abundance of and . The relative abundance of , , and decreased ( < 0.05) over time in high-RFI group. And the relative abundance of in high-RFI group was greater ( < 0.05) than its low-RFI counterpart. Furthermore, RFI had no effect ( > 0.05) on gene expression associated with intracellular pH regulation (, , , , , , , and ) in rumen epithelium and β-hydroxybutyrate metabolism () in both rumen epithelium and liver tissues. In conclusion, even though low-RFI lambs had lower DMI, however, the number of was lower. Additionally, there was no difference in gene expressions level associated with intracellular pH regulation in rumen epithelium between RFI groups.