Strategies to improve the efficiency of beef cattle production

“This suggests that the observed variation in the abundance of a particular bacterial taxa can lead to varied production of short-chain fatty acids, which supply up to 70% of energy to the animal (Bergman 1990).”

“Stoichiometry calculations suggest that enteric CH4 production represents an energetic loss in ruminants of 2%–12% of gross energy intake (Johnson and Johnson 1995).”

“However, given that the composition of the microbiome is overwhelmingly determined by the nature of the diet (Henderson et al. 2015) and the apparent variation in the rumen microbial indicators associated with RFI, their usefulness is yet to be proven.”

“Koch et al. (1963) defined RFI in youthful cattle as the difference between actual feed consumed and predicted feed intake based on maintenance and growth.”

“Although FCR is a superior measurement over average daily gain, FCR metrics do not account for the nutritional value of feed consumed or the human nutritional value placed on the output gain (Mottet et al. 2017).”

“Coprococcus catus was enriched in the rumen of efficient dairy cows that exhibited increased propionate and butyrate production, a shift in fermentation that may reduce the availability of metabolic hydrogen to reduce carbon dioxide to CH4 (Shabat et al. 2016).”

“For example, exosomes in the apoplasts of Arabidopsis leaves were shown to be enriched in defense and stress-related proteins as a result of exposure to abiotic stress (Rutter and Innes 2017).”

“AFEX involves exposing recalcitrant fibre to steam and anhydrous ammonia at high pressure and temperature for 1 h, followed by rapid depressurization and ammonia recovery (Teymouri et al. 2005).”

“(Herd and Arthur 2009; Basarab et al. 2013).”

“Dependant on cattle productive stage, RFI can be used to estimate feed efficiency independent of growth rate, body composition, fat deposition, changes in conceptus weight, milk yield, and milk Published by NRC Research Press composition (Basarab et al. 2003; Basarab et al. 2007).”

“2018), whereas Butyrivibrio, Anaerovibrio (Myer et al. 2015), and Lachnospiraceae, Lactobacillaceae and Veillonellaceae have been associated with less efficient cattle (Li and Guan 2017).”

“Published by NRC Research Press Methanobrevibacter were 2.5 times more abundant in high than low CH4 producing beef cattle, whereas Succinivibrionaceaewere 75.9%more abundant in low than high CH4 producing cattle (Wallace et al. 2015).”

“and a decreased abundance of Methanobrevibacter gottschalkii (Shi et al. 2014).”

“CRISPR technology is more cost effective, precise, and highly efficient compared with other genomic technologies like zinc finger nucleases and transcriptional activator-like effector nucleases (Zhang et al. 2019).”

“In animals, exosomes are secreted mainly by red blood cells, platelets, and lymphocytes (Mandal 2017), and they are present in biological fluids including milk, urine, blood plasma, and amniotic fluid (Keller et al. 2007).”

“Similarly, RFI has been found to be moderately heritable (h2 = 0.16–0.43) in growing cattle (Berry and Crowley 2013).”

“Other genera associated with efficient cattle include Coprococcus (Zhou et al. 2018), whereas Butyrivibrio, Anaerovibrio (Myer et al. 2015), and Lachnospiraceae, Lactobacillaceae and Veillonellaceae have been associated with less efficient cattle (Li and Guan 2017).”

“Similarly, grazed forages, hay, silages, and grains are often contaminated by a wide range of mycotoxins, toxic molecules produced by fungi, often as a result of unfavourable ensiling and storage conditions (Gallo et al. 2015).”

“The Functional Annotation of Animal Genomes project also aims to understand how variation in gene sequences and functional expression determines phenotypic diversity (Andersson et al. 2015).”

“A perennial ryegrass that was selected for higher concentrations of water-soluble carbohydrates, improved milk production and total tract neutral detergent fibre and acid detergent fibre digestibility in dairy cows as compared with conventional ryegrass (Miller et al. 2001).”

“However, an in vitro incubation found that once all 3-NOP is utilized, CH4 production returns to pre-treatment levels within 5 h (Duin et al. 2016).”

“Both confined beef (Carberry et al. 2012; Carberry et al. 2014) and dairy cattle (Jewell et al. 2015) with low RFI had lower proportions of Prevotella within their rumen microbiome.”

“Unlike marker-assisted selection, genomic selection is based on associating thousands of genetic markers spread densely across thousands of reference animals (Hayes and Goddard 2010).”

“2015), although intrinsic relationships between host genetics, rumen microbial population, and phenotypic feed efficiency have also been demonstrated (Guan et al. 2008; Hernandez-Sanabria et al. 2013; Li et al. 2019).”

“For example, monensin was shown to reduce enteric CH4 emissions in the short term, but this reduction was not sustained over 4 wk of continuous administration (Guan et al. 2006).”

“Furthermore, most rumen microbiota have yet to be cultured in the laboratory and characterizing their specific enzymatic and metabolic activities will likely be a key step in defining their impact on feed efficiency (Callaway et al. 2010).”

“Both confined beef (Carberry et al. 2012; Carberry et al. 2014) and dairy cattle (Jewell et al. 2015) with low RFI had lower proportions of Prevotella within their rumen microbiome.”

“Successful gene editing within plants has also been shown using CRISPR technology which has resulted in genetic resistance against fungi, increased yield during drought stress, and increased genetic variation within certain crops (Gao 2018).”

“2017), increased muscling (Proudfoot et al. 2015), and elimination of the horned trait (Carroll et al.”

“Protein turnover, ion pumping associated with Na/K ATPase and mitochondrial proton leakage accounted for 20% of the total inter-animal variation in basal energy expenditure (Bottje and Carstens 2009).”

“Exosomes are vesicles formed within animal and plant cells that are involved in cell communication and Published by NRC Research Press nutrient delivery (Akuma et al. 2019) and have the potential to radically improve efficiency.”

“For example, total rumen transfaunation did not permanently alter the microbiome, with it returning to its original state in some individuals within 7 d (Weimer et al. 2010; Zhou et al. 2018).”

“This combination of physical and chemical treatment disrupts hydrogen, ether, and ester bonds, partially solubilizes lignin, and hydrolyses hemicellulose to a greater extent than conventional alkali treatments (Teymouri et al. 2005; Balan et al. 2009).”

“Understanding the biological and physiological pathways underlying variation in RFI can focus selection on those genes that are most pertinent to efficiency (Cantalapiedra-Hijar et al. 2018; Kenny et al. 2018).”

“Although the beef industry is often criticized for its large consumption of grains, only 7%–13% of world beef production is based upon grainfeeding systems (Gerber et al. 2015; Mottet et al. 2018).”

“…acclimatized to a feed intake measurement system for a 21 d period, followed by a 45–50 d measurement period that requires body weight to be recorded on two consecutive days at the beginning, end, and at regular intervals throughout the feeding period (Manafiazar et al. 2017; Kenny et al. 2018).”

“Climate change influences crop production through altered weather patterns, increased soil salinity, drought, and susceptibility to disease and insect attack (Haque et al. 2018).”

“Bacteria frequently associated with BRD include Mannheimia haemolytica, Pasteurella multocida, Histophilus somnus, Pasteurella multocida, Trueperella pyogenes, and Mycoplasma bovis (Klima et al. 2014; Zeineldin et al. 2019).”

“Alkali treatments including ammonia, sodium hydroxide, oxidative lime, calcium oxide, and calcium hydroxide have been successfully employed to increase ruminal fibre degradation and the nutritional value of lowquality feeds (Chang et al. 2001; Adesogan et al. 2019).”

“In a further evaluation of 5976 feedlot cattle, BRD was associated with a 0.37 kg d−1 loss in average daily gain and a reduction in carcass weight of 8.16 kg (Schneider et al. 2009).”

“(Herd and Arthur 2009; Basarab et al. 2013).”

“Carcass size of slaughter cattle was approximately 250 kg, and this trend only started to be reversed in the early 1970s due to the selection for increased growth rate and larger framed cattle through cross breeding (Berg 1975; Berg et al. 1979; Gregory and Cundiff 1980; Fredeen et al. 1981).”

“Mechanical processing including chopping, shredding, and pelleting can increase the surface area for microbial attachment, reduce gut fill, and increase feed intake (Adesogan et al. 2019).”

“It is theorized that a 20% increase in reproductive rate of the cow herd would reduce the total feed energy requirement per kilogram of edible product by approximately 12% (Dickerson 1978).”

“Similarly, the use of artificial insemination and other breeding technologies is limited, slowing the rate of genetic progress (Burns et al. 2010).”

“Alternatively, the CH4 inhibitor 3-NOP is extremely effective in inhibiting the activity of methanogens within the rumen if it is administered daily with no evidence of adaptation (Jayanegara et al. 2018).”

“Cattle with larger frame and carcass weight divert energy towards production more efficiently than smaller framed animals that divert more energy towards Published by NRC Research Press maintenance (Castro Bulle et al. 2007).”

“Bovine respiratory disease is the most common cause of morbidity and mortality in feedlot cattle, resulting in production, welfare, and economic losses (Holman et al. 2015).”

“Recent work has estimated that approximately 20% of the variation in production and efficiency traits in beef cattle (i.e., average daily feed intake, average daily gain, and FCR) were explained by variation in the microbiome (Paz et al. 2018).”

“Dependant on cattle productive stage, RFI can be used to estimate feed efficiency independent of growth rate, body composition, fat deposition, changes in conceptus weight, milk yield, and milk Published by NRC Research Press composition (Basarab et al. 2003; Basarab et al. 2007).”

“Similarly, the addition of 3-NOP to a high forage diet resulted in a consistent reduction in CH4, though once removed, CH4 production returned to pre-treatment levels (Romero-Perez et al. 2015).”

“Alternatively, although deep nasophyaryngeal and pharyngeal swabs revealed shifts in bacterial taxa between healthy and BRD calves, there was no difference in the diversity of the microbial community (Lima et al. 2016; Zeineldin et al. 2017).”

“Additionally, selection for low RFI had no effect on calving, pregnancy, or weaning rates (Arthur et al. 2005; Basarab et al. 2011; Callum et al. 2018).”

“Although the beef industry is often criticized for its large consumption of grains, only 7%–13% of world beef production is based upon grainfeeding systems (Gerber et al. 2015; Mottet et al. 2018).”

“Other genera associated with efficient cattle include Coprococcus (Zhou et al. 2018), whereas Butyrivibrio, Anaerovibrio (Myer et al.”

“taurus breeds are cold tolerant and produce higher quality beef (Rodrigues et al. 2017).”

“, uterine environment and colostrum) influence the genetic susceptibility of the offspring to respiratory disease (Snowder et al. 2005).”

“the rumen being exceeded by the production of organic acids (Nikkhah 2012).”

“Commensal bacteria can inhibit the proliferation of bacterial pathogens through competition for nutrients, competitive exclusion, and the production of antimicrobials (Zeineldin et al. 2019).”

“In calves diagnosed with BRD, the respiratory tract microbiome was shown to be characterised by a reduction in bacterial richness and evenness (Holman et al. 2015; Timsit et al. 2018).”

“However, these quantitative trait loci are defined as population specific and have little overlap with other populations of cattle (Saatchi et al. 2014).”

“GHR encodes for a receptor for growth hormone which influences growth, function and metabolism, and cellular storage of carbohydrates, proteins, and lipids (Di Stasio et al. 2005).”

“Similarly, respiratory disease was found to be negatively correlated with average daily gain, marbling score, and hot carcass weight across 18 feedlots over 5 yr (Reinhardt et al. 2009).”

“Enzyme application, unlike other dietary additives, must also compete with digestion rates and ruminal residence times to be effective within the rumen (Terry et al. 2019).”

“Across multiple studies (Ribeiro et al. 2016a; Tirado-González et al. 2018; Terry et al. 2019), it is consistently reported that the effects of enzymes varies and is confounded by multiple factors including enzyme type, specificity, rate of application, and dietary composition.”

“Similarly, although some studies suggest that the decrease in CH4 with 3-NOP results in energetic savings being redirected towards body weight gain, these findings are not consistent with some studies reporting that 3-NOP increased H2 eructation (Vyas et al. 2016).”

“This could be a concern for feedlot cattle rapidly transitioned from a forage to a concentrate diet and for grazing cattle consuming a diverse range of forage species (Belanche et al. 2019).”

“In a GWAS, Holstein cattle with superior antibody-mediated and cell-mediated immune responses were genotyped using the Illumina Bovine SNP50 BeadChip (Thompson-Crispi et al. 2014).”

“Alternatively, although deep nasophyaryngeal and pharyngeal swabs revealed shifts in bacterial taxa between healthy and BRD calves, there was no difference in the diversity of the microbial community (Lima et al. 2016; Zeineldin et al. 2017).”

“Similarly, two transfers of rumen contents from bison into beef cattle increased the diversity and evenness of the bacterial communities in the rumen 1 and 27 d after rumen transfer (Ribeiro et al. 2017), but some phylum quickly returned to pre-transfer abundances.”

“Similarly, a single dose of bromochloromethane to pre-weaned goat kids resulted in a change in the methanogen population that persisted for 3 mo (Abecia et al. 2014).”

“2015), although intrinsic relationships between host genetics, rumen microbial population, and phenotypic feed efficiency have also been demonstrated (Guan et al. 2008; Hernandez-Sanabria et al. 2013; Li et al. 2019).”

“Excessive processing of barley and wheat increased DMI and decreased gain-to-feed ratio, salable meat yield, and rib eye area in feedlot steers fed a high grain diet (Moya et al. 2011; Ribeiro et al. 2016b).”

“%) in feed-efficiency traits (Abo-Ismail et al. 2018).”

“In Canada, over 75% of malt barley fails to make the quality grade required for human consumption and is relegated to livestock feed (Ribeiro et al. 2016b).”

“These SNPs were mapped to six putative candidate genes that had biological functions related to the regulation of gene expression, glucose and lipid metabolism, and fat deposition (Akanno et al. 2018).”

“Bacterial communities found in the upper respiratory tract of dairy calves were highly similar to those found with the vaginal canal of the dam, with 73%–87% of operational taxonomic units being shared at 3, 14, and 35 d after calf birth (Lima et al. 2019b).”

“For example, the microbiome of lambs was shown to be altered when lambs were fed linseed oil during pre-weaning with this change persisting for 10 wk after linseed oil supplementation ceased (Lyons et al. 2017).”

“For example, composite breeds of B. indicus and B. taurus are kept in housing in tropical countries to improve milk production efficiency as a result of a reduction in environmental stressors such as parasites and heat (O’Neill et al. 2010).”

“Although ruminants in sub-Sahara Africa frequently have reproduction rates of less than 50%, they provide milk and protein to stakeholders with little to no input (Otte et al. 2019).”

“If these animals are removed from these controlled environments, they face adverse effects on health and mortality (El-Deek and El-Sabrout 2019).”

“For growth and carcass traits, MBVs accounted for up to 18% and 8%, respectively, of genetic variation in a multi-breed analysis, and up to 28% and 42%, respectively, in single breeds of beef cattle (Weber et al. 2012).”

“…employed to modify alleles so as to allow the expression of genetically engineered cattle that would produce leukocytes resistant to leukotoxin-induced cytolysis, demonstrating the feasibility of breeding lines of cattle genetically resistant to Mannheimia haemolytica (Shanthalingam et al. 2016).”

“barley to a lower PI were more feed efficient than those fed barley with a higher PI (Wang et al. 2003).”

“Similarly, dried distillers’ grain readily replaces cereal grains in ruminant diets due to its rich energy and protein content (Hünerberg et al. 2014).”

“…cattle (<1 calf cow−1 yr−1) compared with chickens (∼180 eggs hen−1 yr−1) and even pigs (∼20 piglets sow−1 yr−1) also slows the rate of genetic progress and, therefore, plays a major role in the slow rate of efficiency gains obtained via genetic selection (Nielsen et al. 2013; Zuidhof et al. 2014).”

“A meta-analysis of GWAS revealed a common pathway of genes involved in valine, leucine, and isoleucine catabolism that were related to RFI in three metagenomic studies (Duarte et al. 2019) and one transcriptomic study (Khansefid et al.”

“Modulation of the disease through use of natural microflora inhabiting the respiratory tract was recently investigated (Amat et al. 2019).”

“A single dose of a intranasal probiotic consisting of a mixture of six Lactobacillus strains reduced nasal colonisation of Mannheimia haemolytica in dairy calves (Amat et al. 2020) and caused no adverse effects on the health and growth performance of beef calves (Amat et al. 2020).”

“The Canadian Cattle Genome Project is a large-scale international initiative that was employed to develop genomics-based tools for genetic selection to increase the efficiency and sustainability of dairy and beef cattle production (Stothard et al. 2015).”

“Feeding AFEX-treated rice straw to lactating dairy cows increased neutral detergent fibre intake and milk production when included in the diet at 7% of dry matter (Weimer et al. 2003).”

“2015), and elimination of the horned trait (Carroll et al. 2016).”

“2019) and one transcriptomic study (Khansefid et al. 2017).”

“Similarly, compared with control lines, in vitro dry matter and neutral detergent fibre digestibility were increased in two lignin down-regulated alfalfa lines (Getachew et al. 2018).”

“Increasing the degree of processing of barley (slight, medium, and crushed) improved feed conversion efficiency by 10% in beef bulls fed a high-concentrate diet (Mathison et al. 1997).”

“Research has been conducted to differentiate the cargo profiles of exosomes as influenced by dairy cows differing in metabolic health (Crookenden et al. 2016), uterine health, and fertility status (Koh et al.”

“2016), uterine health, and fertility status (Koh et al. 2018; Mitchell et al. 2020).”

“For example, incorporation of unsalable carrot or pumpkin waste at up to 40% of dry matter in ensiled corn or sorghum did not alter silage quality and improved in vitro dry matter digestibility (Forwood et al. 2019; Hooker et al. 2019).”

“The AFEX treatment of barley straw, wheat straw, corn stover, and rice straw increased in vitro dry matter disappearance by up to 128% (Beauchemin et al. 2019).”

“Carcass size of slaughter cattle was approximately 250 kg, and this trend only started to be reversed in the early 1970s due to the selection for increased growth rate and larger framed cattle through cross breeding (Berg 1975; Berg et al. 1979; Gregory and Cundiff 1980; Fredeen et al. 1981).”

“Both confined beef (Carberry et al. 2012; Carberry et al. 2014) and dairy cattle (Jewell et al. 2015) with low RFI had lower proportions of Prevotella within their rumen microbiome.”

“Single-nucleotide polymorphism (SNP) panels are a genomic tool that can predict genomic breed composition, retained heterozygosity, and heterosis of beef cattle (Akanno et al. 2017).”

“Similarly, AFEX-treated barley straw increased dry matter, neutral detergent fibre, and acid detergent fibre degradation, whilst also reducing CH4 produced per gram digested dry matter in an artificial rumen (Griffith et al. 2016).”

“non-treated wheat straw, AFEX treatment increased intake, digestibility, and milk production in lactating buffalo and crossbred dairy cattle (Mor et al. 2018).”

“This resulted in a beef population that was dominated by smaller, compact animals with increased prevalence of dwarfism genes (Willham 1982).”

“These gains equated to a CA$161 increase in yearly profit per heifer when averaged over five parities in an intensive beef production system (Basarab et al. 2018).”

“…acclimatized to a feed intake measurement system for a 21 d period, followed by a 45–50 d measurement period that requires body weight to be recorded on two consecutive days at the beginning, end, and at regular intervals throughout the feeding period (Manafiazar et al. 2017; Kenny et al. 2018).”

“Tempering barley improved milk yield, feed efficiency, and digestibility of starch by 5%, 10%, and 4%, respectively, compared with dry rolling in dairy cows (Christen et al. 1996).”

“Carcass size of slaughter cattle was approximately 250 kg, and this trend only started to be reversed in the early 1970s due to the selection for increased growth rate and larger framed cattle through cross breeding (Berg 1975; Berg et al. 1979; Gregory and Cundiff 1980; Fredeen et al. 1981).”

“In Canada, over 75% of malt barley fails to make the quality grade required for human consumption and is relegated to livestock feed (Ribeiro et al. 2016b).”

“For example, incorporation of unsalable carrot or pumpkin waste at up to 40% of dry matter in ensiled corn or sorghum did not alter silage quality and improved in vitro dry matter digestibility (Forwood et al. 2019; Hooker et al. 2019).”

“2016), uterine health, and fertility status (Koh et al. 2018; Mitchell et al. 2020).”

“For example, replacement of soybean meal with soybean cake had no effect on DMI, volatile fatty acid production, or apparent digestibility Published by NRC Research Press in dairy cows (Silveira et al. 2019).”

“selection for these traits is achievable (Berry 2014).”

“MBVs predicted up to 35% of observed variability in carcass traits with a prediction range from 0.43 to 0.59 across beef cattle breeds (Akanno et al. 2019).”

“The host itself plays an important role in causing physical damage to feed through mastication and rumination, breaching physical barriers that impede the rapid colonisation of feed by rumen microbiota (Terry et al. 2020).”

“…monogastric by producing 1 kg meat by consuming 2.8 kg food as compared to monogastric producing the same quantity of meat by consuming 3.2 kg food (Terry et al. 2020, 2021), but if we consider the volume of dry matter consumed, then ruminants produce 1 kg animal protein by consuming 133 kg dry…”

“Numerous challenges face the beef industry including needs for improved nutrition and production efficiency to feed a growing human population [1,2].”