Research Project: Improve Nutrient Management and Efficiency of Beef Cattle and Swine

Location: Nutrition, Growth and Physiology

2021 Annual Report

Objectives
Objective 1: Determine the effects of dietary changes on efficiency of growth and nutrient utilization of beef cattle and swine. Sub-objective 1A: Prediction of dry matter intake from neutral detergent fiber concentration. Sub-objective 1B: Determine the effects of feed additives on feed efficiency. Sub-objective 1C: Evaluate the use of an antibiotic alternative in swine. Objective 2: Improve determination of dynamic changes in nutrient requirements as the animal's physiological status changes to allow for timed nutrient delivery. Objective 3: Use novel forage systems for growing and maintaining beef cattle. Objective 4: Determine metabolic and physiological mechanisms responsible for variation in feed efficiency that is under genetic control. Sub-objective 4A: Evaluate genetic relationships with feed efficiency. Sub-objective 4B: Effects of metabolites and hormones on feed efficiency. Sub-objective 4C: Relationships between mitochondrial function and feed efficiency. Objective 5: Determine the environmental factors that contribute to the variation in feeding behavior, growth, and well-being of livestock. Sub-objective 5A: Novel methods for early detection of illness. Sub-objective 5B: Relationships between swine feeding behavior with feeder size and placement. Sub-objective 5C: Effects of weather on cattle well-being and feeding behavior.

Approach
Feed costs represent the single largest input in both beef and swine production; however, less than 20% of the energy from feed is converted to edible product. Improving the efficiency that feed is converted to animal products has the potential to improve the economic efficiency of animal production while also improving the sustainability of animal agriculture. To maximize feed efficiency the correct profile of nutrients are matched to meet an animal’s needs for its current biological status (growth, pregnancy, lactation, previous nutrient history, and disease). In order to provide the correct profile of nutrients, the nutrient composition of feeds and the dynamic nutrient requirements of the animal must both be identified and then synchronized. There is genetic variation among animals in their ability to utilize feed. Multiple genes are associated with the regulation of feed intake, weight gain, and the utilization of ingested nutrients. Differential expression of these genes results in variation of feed efficiency among animals within populations, and these genetic differences potentially change the nutrient requirements of the animal. Identifying the role of nutrition in regulating gene expression and the mechanisms by which efficient animals utilize nutrients is needed to develop nutrition management strategies. In addition to variation in physiological responses, there is a need to understand genetic and environmental variation in animal feeding behavior that lead to variation in nutrient utilization.

Progress Report
Objective 1: Thirty-two sows and 352 pigs from their litters were utilized to determine the efficacy of a commensal fungi, K. slooffiae, as a growth promotant in pigs. Performance parameters, gut morphology, gut histology, pathogen shedding, the mycobiome, and the bacteriome are being measured. Objective 2: Mature cows (n=120) were fed four different levels of Vitamin A during gestation and lactation to determine Vitamin A requirements in cows eating harvested forages. Yearling bulls on two rates of gain (n=37) are being evaluated. The effects of two rates of gain on sperm function, bull performance, and subsequent calf performance are being measured. Heifers that are individually supplemented with 0.91 kg distillers grains or not receiving supplementation on pasture (n=250) are being evaluated for the effect of supplementation on performance, fertility, and subsequent calf performance. Objective 3: Cows in two fall calving production systems (n=293 cows) are being evaluated. Feed and forage intake are being measured and reproductive efficiency and calf growth rates are being measured. Two types of cover crops and traditional calf fed systems (n=357 steers) are being evaluated for their influence on growth and meat quality. Heifers fed arginine, methionine, or the combination (n=36) during the periconceptual period of gestation are being evaluated for effects on improving embryonic development. Objective 4: Feed efficiency phenotypes were collected from approximately 1000 grow/finish pigs in the Clay Center, Nebraska, Feed Efficiency Barn. These data will be used for genomic analyses, correlation with reproductive traits, correlation with the microbiome, as well as other studies. Rumen and white blood cell RNA-sequencing libraries were generated for 16 heifers with variation in feed efficiency on forage diets to identify genes that are differentially expressed. A feed efficiency panel for 36 genetic variants has been generated and tested on 112 pigs with feed efficiency phenotypes. The white blood cells of 192 pigs with feed efficiency data have been sequenced for gene expression to determine whether there are gene profiles indicative of animals with superior phenotypes. The data is currently being analyzed. Objective 5: White blood cell RNA-sequencing libraries were created for 33 cattle that were either sick with bovine respiratory disease or were case control animals at 3 time points that included pre-conditioning, weaning and sick or case control to identify whether there are gene expression profiles that are predictive of animals that are more susceptible to illness.

Accomplishments
1. The genetic composition of cattle is associated with differences in rumen bacterial communities. Microbes in the cattle rumen are responsible for breaking down feed and forage consumed into nutrients that the animal can use. These microbial communities vary widely from animal to animal, and it has been shown in other species that the animal’s genetics contributes to this difference. ARS scientists at Clay Center, Nebraska, in collaboration with the University of Nebraska-Lincoln, determined which regions of the chromosomes corresponded to rumen bacterial community composition. Regions near genes involved in absorption of the nutrients produced by the bacteria were identified. This study demonstrated that there is a relationship between the cattle (host) genome and the rumen bacterial community composition. This study suggests that optimizing rumen microbial profiles for feed efficiency will need to be done in conjunction with the genetic selection of animals that support preferred profiles.

2. Relationships between rumen physiology and liver abscesses in beef cattle were determined. Beef cattle liver abscesses are the highest cause of liver condemnation and costs the beef industry approximately $64 million annually. In addition to removing these livers from the food chain, abscesses reduce feed intake, body weight gain, carcass weight and may also affect cattle well-being. Liver abscess is caused by the colonization of bacteria released from the rumen and transported to the liver through the portal vein. ARS scientists at Clay Center, Nebraska, in collaboration with the University of Nebraska-Lincoln, identified over 200 genes, enriched in inflammation and protein translation pathways in the rumen from animals with liver abscesses. Differences were also identified in bacterial communities attached to the rumen of animals with liver abscesses. Unique correlations between differentially expressed genes and bacterial species attached to the rumen were identified in animals with liver abscesses. This is the first study to show that the changes in the rumen tissue associated with liver abscesses are maintained well after the early development of rumen acidosis caused by high corn diets. These differences provide insight into the mechanisms of liver abscess development in cattle and may serve as biomarkers for the identification of animals with liver abscesses in feedlot cattle.

3. Current cattle diets require new models to predict metabolizable energy in feed. Metabolizable energy (ME) of feed is used to accurately determine the amount of feed needed to meet an animal’s energy requirement. It is difficult to measure and is usually estimated from digestible energy (DE), which is more easily measured. Historically, it has been assumed that metabolizable energy was 82% of digestible energy. However, the diets of beef cattle have changed since this assumption was made and metabolizable energy is underestimated on modern diets. A study by ARS scientists at Clay Center, Nebraska, and collaborators at Texas A&M and Texas Tech Universities, was conducted to determine the relationships between the forage-to-concentrate ratio of the diet and the relationship between metabolizable and digestible energy. Results indicate that low-forage diets provide cattle with more metabolizable energy than predicted per amount of feed because less digestible energy is lost in waste products. The existing model to predict metabolizable energy from digestible energy content is not adequate for current cattle diets. New models have been developed using this data set and others collected by these researchers and others to evaluate their ability to predict ME from DE on diets currently being fed. These models will more accurately predict nutrient value of the feed and expected growth of the animals, which, allows producers to evaluate value of feedstuffs, manage time on feed, and harvest dates.

4. Altering heifer growth patterns does not affect lifetime production. Slowing growth before puberty followed by increased growth around puberty has been demonstrated to change both the number of eggs on the ovary early in life, and lifetime milk production. ARS scientists at Clay Center, Nebraska, conducted a long-term study and determined there was no difference in the total weight of calves weaned and no difference in the number of original cows retained at the end of the study. Heifers do not need to be fed excessive amounts of feed that lead to obesity to improve production efficiency. Lower inputs of less expensive feeds can be utilized in development.

5. Ferric citrate fed to cattle does not reduce methane production. Ruminants are a source of methane emitted to the environment. In cattle, methane production represents both a loss of feed energy and a greenhouse gas. It had been hypothesized that feeding ferric acid, which binds to hydrogen, might reduce the amount of methane produced by feedlot cattle. ARS scientists at Clay Center, Nebraska, in collaboration with the University of Tennessee and Iowa State University, added different levels of ferric citrate to steer diets and evaluated the animals for enteric methane production and rumen fluid microbial compositions. The addition of ferric citrate to the diet had no impact on the rumen microbial communities, the concentrations of rumen methanogens, and enteric methane production. The addition of ferric acid to the diets of feedlot cattle is not a viable option for reducing methane production in beef feedlot cattle.

6. Maternal nutrition does not affect nutrient transporters in the uterus in early pregnancy. Beef heifers are bred and typically conceive 90% of the time; however, only 50% of those bred heifers maintain a pregnancy. Therefore, many heifers must be rebred several times to maintain a pregnancy which results in decreased efficiency of livestock production. There is little data available to determine how changes in maternal nutrition affect embryonic development and maintenance of pregnancy. ARS scientists at Clay Center, Nebraska, in collaboration with North Dakota State University, evaluated the gene expression and protein levels of five uterine transporters in heifers on restricted feed and those on unrestricted control diets. Results indicated that maternal nutrition had no effect on nutrient transporters during early pregnancy, rather embryonic metabolism may be altered with reduced nutrient availability. These data suggest that while feed restriction of pregnant heifers may not affect heifer metabolism during early gestation, it may change the metabolism of the developing calf, which will affect lifetime productivity in the herd.

7. Maternal nutrient restriction in early pregnancy alters fetal gene expression. Under nutrition during fetal development can result in smaller and less healthy calves; however, the mechanisms are poorly understood. ARS scientists at Clay Center, Nebraska, in collaboration with the North Dakota State University, evaluated the expression of genes in the fetal brain, liver, and muscle tissues to better understand the mechanisms responsible for changes to the fetus by maternal feed restriction. Results indicate that maternal nutrient restriction alters regulation of genes that negatively affect the development of skeletal muscle tissue and nutrient sensing pathways. These results identified major regulators that affect fetal tissue gene expression and produced new biological systems level insights into fetal responses to maternal feed restriction. This study showed that heifer feed restriction early in pregnancy results in changes to calf metabolism and economically important tissues like skeletal muscle. Therefore, greater emphasis should be placed on management and nutrient delivery to heifers during early gestation.

Review Publications
Hales, K.E., Tait Jr, R.G., Lindholm-Perry, A.K., Cushman, R.A., Freetly, H.C., Brown-Brandl, T.M., Bennett, G.L. 2020. Effects of the F94L Limousin associated myostatin gene marker on metabolic index in growing beef heifers. Applied Animal Science. 36(6):851-856. https://doi.org/10.15232/aas.2020-02046.
Clemmons, B.A., Schneider, L.G., Melchior, E.A., Lindholm-Perry, A.K., Hales, K.E., Wells, J., Freetly, H.C., Hansen, S.L., Drewnowski, M.E., Hartman, S.J., Myer, P.R. 2021. The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea, and methane production in growing beef steers. Access Microbiology. 3(1). Article 000180. https://doi.org/10.1099/acmi.0.000180.
Abbas, W., Keel, B.N., Kachman, S.D., Fernando, S.C., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K. 2020. Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses. Journal of Animal Science. 98(12):1-13. https://doi.org/10.1093/jas/skaa359.
Diniz, W.J., Crouse, M.S., Cushman, R.A., McLean, K.J., Caton, J.S., Dahlen, C.R., Reynolds, L.P., Ward, A.K. 2021. Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy. Scientific Reports. 11. Article 2771. https://doi.org/10.1038/s41598-021-82156-w.
Crouse, M.S., McLean, K.J., Dwamena, J., Neville, T.L., Menezes, A.C.B., Ward, A.K., Reynolds, L.P., Dahlen, C.R., Neville, B.W., Borowicz, P.P., Caton, J.S. 2021. The effects of maternal nutrition during the first 50 d of gestation on the location and abundance of hexose and cationic amino acid transporters in beef heifer uteroplacental tissues. Journal of Animal Science. 99(1):1-12. https://doi.org/10.1093/jas/skaa386.
Abbas, W., Howard, J.T., Paz, H.A., Hales, K.E., Wells, J., Kuehn, L.A., Erickson, G.E., Spangler, M.L., Fernando, S.C. 2020. Influence of host genetics in shaping the rumen bacterial community in beef cattle. Scientific Reports. 10. Article 15101. https://doi.org/10.1038/s41598-020-72011-9.
Abedal-Majed, M.A., Kurz, S.G., Springman, S.A., McNeel, A.K., Freetly, H.C., Largen, V., Magamage, M., Sargent, K.M., Wood, J.R., Cushman, R.A., Cupp, A.S. 2020. Vascular endothelial growth factor A isoforms modulate follicle development in peripubertal heifers independent of diet through diverse signal transduction pathways. Biology of Reproduction. 102(3):680-692. https://doi.org/10.1093/biolre/ioz211.
Caton, J.S., Engle, T., Crouse, M.S., Archibeque, S., Nagaraja, T.G., Huntington, G. 2020. Frontiers in ruminant nutrition: An ASAS-CSAS-WSASAS 2020 symposium overview. Journal of Animal Science. 98(9):1-3. https://doi.org/10.1093/jas/skaa276.
Caton, J.S., Crouse, M.S., McLean, K.J., Dahlen, C.R., Ward, A.K., Cushman, R.A., Grazul-Bilska, A.T., Neville, B.W., Borowicz, P.P., Reynolds, L.P. 2020. Maternal periconceptual nutrition, early pregnancy, and developmental outcomes in beef cattle. Journal of Animal Science. 98(12):1-16. https://doi.org/10.1093/jas/skaa358.
Fuller, A.L., Wickersham, T.A., Sawyer, J.E., Freetly, H.C., Brown-Brandl, T.M., Hales, K.E. 2020. The effects of the forage-to-concentrate ratio on the conversion of digestible energy to metabolizable energy in growing beef steers. Journal of Animal Science. 98(8)1-10. https://doi.org/10.1093/jas/skaa231.
Keel, B.N., Oliver, W.T., Keele, J.W., Lindholm-Perry, A.K. 2020. Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library. Animal Gene. 17-18. Article 200105. https://doi.org/10.1016/j.angen.2020.200105.
Parker, D.B., Casey, K.D., Hales, K., Waldrip, H., Min, B., Cortus, E., Woodbury, B.L., Spiehs, M.J., Meyer, B.E., Willis, W.M. 2020. Toward modeling of nitrous oxide emissions following precipitation, urine and feces deposition on beef cattle feedyard surfaces. Transactions of the ASABE. 63(5):1371-1384. https://doi.org/10.13031/trans.13847.
Smith, W.N., Brake, D.W., Lindholm-Perry, A.K., Oliver, W.T., Freetly, H.C., Foote, A.P. 2020. Associations of mucosal disaccharidase kinetics and expression in the jejunum of steers with divergent average daily gain. Journal of Animal Science. 98(9):1-6. https://doi.org/10.1093/jas/skaa285.
Snelling, W.M., Hoff, J.L., Li, J.H., Kuehn, L.A., Keel, B.N., Lindholm-Perry, A.K., Pickrell, J.K. 2020. Assessment of imputation from low-pass sequencing to predict merit of beef steers. Genes. 11(11). Article 1312. https://doi.org/10.3390/genes11111312.
Wells, J., Berry, E.D., Kim, M., Bono, J.L., Oliver, W.T., Kalchayanand, N., Wang, R., Freetly, H.C., Means, W.J. 2020. Determination of gastrointestinal tract colonization sites from feedlot cattle transiently shedding or super-shedding Escherichia coli O157:H7 at harvest. Journal of Applied Microbiology. 129:1419-1426. https://doi.org/10.1111/jam.14684.
Bennett, G.L., Thallman, R.M., Snelling, W.M., Keele, J.W., Freetly, H.C., Kuehn, L.A. 2021. Genetic changes in beef cow traits following selection for calving ease. Translational Animal Science. 5(1):1-10. https://doi.org/10.1093/tas/txab009.
Smock, T.M., Samuelson, K.L., Wells, J.E., Hales, K.E., Hergenreder, J.E., Rounds, P.W., Richeson, J.T. 2020. Effects of Bacillus subtilis PB6 and/or chromium propionate supplementation on serum chemistry, complete blood count, and fecal Salmonella spp. count in high-risk cattle during the feedlot receiving and finishing periods. Translational Animal Science. 4(3):1-11. https://doi.org/10.1093/tas/txaa164.
Freetly, H.C., Cushman, R.A., Bennett, G.L. 2021. Production performance of cows raised with different postweaning growth patterns. Translational Animal Science. 5(3):1-7. https://doi.org/10.1093/tas/txab031.