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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Research Project #433503

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

2020 Annual Report

Objective 1: Evaluate the gastrointestinal microbial and digestive factors that influence nutrient use efficiency and milk production capacity and quality in dairy cattle. • Sub-objective 1.A. Determine the relationship between the gastrointestinal microbial community composition and production capacity and efficiency; develop relevant strategies to direct rumen microbial community composition for increased milk production capacity and efficiency and improved milk quality. • Sub-objective 1.B. Evaluate dietary composition, microbial, and animal factors, and microbe-animal interactions that affect the digestion and metabolism of forage/feed by rumen microbes and the passage of digesta from the rumen to predict nutrient provisions for increased performance and nutrient use efficiency. Objective 2: Identify animal factors that affect the conversion of dietary and potentially digestible nutrients toward milk production for increased nutrient use efficiency. • Sub-objective 2.A. Evaluate the dairy cow genetic and genomic factors affecting nutrient use efficiency and their interactions with the gastrointestinal microbial community and dietary factors for increased milk production capacity and efficiency and improved milk quality. • Sub-objective 2.B. Optimize the profile of circulating nutrients and identify and improve the genetic and management related-animal factors that affect the partitioning of nutrients toward milk and away from manure and greenhouse gas emissions.

Sub-objective 1.A will develop biological resources and computational tools to enhance characterization of dairy breed-specific bovine and other genomes. Samples will initially be taken from a healthy cow in early lactation that has been exclusively fed mixed forage (alfalfa- and corn-silage based); samples will come from three separate portions of the rumen (solid, liquid, and epimural lining). Our plan is to sequence and assemble the most prevalent species/strains that occupy the solid (feed particle-associated) and liquid (planktonic) phases of rumen digesta, and the interior rumen lining (epimural community). Additionally, establishment and the potential to direct the rumen microbial community toward a feed efficient phenotype will be studied in dairy calves. Multiple doses of rumen fluid from cows having a particular milk production efficiency status will be provided to newborn and pre-weaned calves. We will evaluate if this results in the establishment of a microbial community that is more similar to that of the donor inoculum than in calves dosed with sterile rumen fluid. These heifers will be followed through their first lactation to evaluate if the dosed animals will exhibit milk production efficiency more like that of the donor cow than that of the controls. Sub-objective 1.B will consist of several in vitro studies to evaluate methods of analyzing for microbial protein, starch degradability, and microbial protein synthesis. In addition to the in vitro studies, a series of animal experiments will be conducted to evaluate within-day changes in rumen liquid volume and passage that occur in response to multiple dietary factors that alter water intake and outflow of liquid from the rumen. Water intake will also be monitored to evaluate the effect of treatment and the potential correlation with rumen liquid passage. Sub-objective 2.A will involve several studies to identify molecular markers and adaptive transcriptome changes in dairy cows in response to diet, health status, and the interaction between rumen microbiome diversification and host transcriptome and genetic profile. Host transcriptome changes will be evaluated from a diverse range of tissue and sample types. Sub-objective 2.B will use several lactation and nutrient balance studies to evaluate nutrient partitioning in response to dietary provision of different levels of protein. We will collect nitrogen balance, gaseous emission, and production measurements to determine the effects of nutritional treatment on productivity and environmental output.

Progress Report
Ruminal microbes provide dairy cows the ability to extract energy from cellulosic plant material and microbial matter is also an important source of nutrients for dairy cows. These microbes also influence the composition, especially the fat composition, of milk. However, it is very difficult to identify and measure these microbes in whole herds of cattle so that changes in microbial profile can be associated with optimal milk production. We have been conducting an ongoing study to explore the use of non-invasive swabbing of the cow's mouth to identify rumen microbe communities as a large-scale population study (Subobjective 1.A). Initial results demonstrate that this method is efficient and was suitable for routine analysis. This method is promising to allow large-scale application for selecting for cows with better rumen microbial profiles. Use of digesta markers are essential for measuring passage of liquid and associated nutrients from the rumen in dairy cattle (Hypothesis 1.B.3). Because commonly used markers have flaws that recommend against their use, we worked with an alternative liquid marker, polyethylene glycol (PEG). Finding unexpected technique-specific challenges with the widely used assay required substantial time and effort to make modifications to increase reliability. Previous work in nonruminants offered a useful modification that we evaluated in rumen fluid. We have now developed an assay for PEG that is much less technique-sensitive, is likely to give more consistent analytical values for measuring ruminal kinetics, and would be useful to the wider ruminant nutrition community. An invention to produce ruminally available soluble peptides was previously developed that improved the digestibility of the treated feedstuff and modified microbial use of carbohydrates, suggesting a more efficient use of the feed. We evaluated several quality control methods to assess quality of the modified feedstuff designed to improve microbial use and efficiency of utilizing feed carbohydrates and protein (Subobjective 1.B). We have obtained an innovation grant to support animal studies with the invention, which are in the planning stages. Field nutritionists and commercial laboratories were in contact with us regarding analyses for water-soluble carbohydrates (WSC) and starch that, when summed, were extraordinarily high for the particular corn-derived feeds (Subobjective 1.B). The issue was the evolution of maltodextrins in the feeds, which are detected as both starch and WSC in the assays, resulting in this material being counted twice. We developed an approach for analysis of water-soluble starch that places this fraction with carbohydrates of similar fermentation characteristics. We have discussed and disseminated the assay with commercial feed analysis laboratories. We evaluated the ability of a widely used nutritional model, the Cornell Net Carbohydrate and Protein System, to predict the actual milk production performance of cows on research diets varying in carbohydrate source and ruminal protein degradability (Subobjective 1.B). We discovered that the model typically over- or underestimated milk production by 2 to 4 kg of milk per day. Surprisingly, regression evaluation using other model outputs showed an equation incorporating rumen excesses of grams of nitrogen from peptides or ammonia to predict milk production to within approximately 0.5 kg across all diets. The basis within the nutritional model for this close estimation is being further evaluated. While dairy cow nutrient requirements may change throughout the course of lactation, often cows are fed the same diet for the entire lactation. Precision feeding dietary protein throughout lactation would increase nutrient use efficiency while reducing environmental nitrogen load on dairy farms. We conducted a study to evaluate the effects of feeding different levels of dietary crude protein (CP) at different stages of lactation (Subobjective 2.B). Across all four stages of lactation, cows fed diets containing 16.5% CP resulted in maximized levels of milk protein secretion. Increasing dietary CP beyond 16.5% did not result in additional increases in milk production across lactation. Additionally, increasing CP to 18% in late lactation was detrimental to productivity. Nitrogen use efficiency was reduced linearly with increasing dietary CP and for cows in late lactation for all levels of dietary CP. These results will allow dairy producers and nutritionists to optimize dietary protein feeding throughout lactation. Different breeds of cattle are the result of many generations of genetic selection for specifically desired traits. The United States dairy herd population is currently comprised of several breeds with low proportions, while Holstein is the predominant dairy breed. The number of Jersey cows and herds has been increasing in recent years and Jersey cows are often considered to have greater feed efficiency due to their lower body weight and higher milk components, although the literature is equivocal on the point. We have initiated several studies to evaluate nutritional and physiological differences between Holstein and Jersey cows (Subobjective 2.B). First and second parity, Holstein and Jersey cows were evaluated for 84 days after calving for early lactation performance and feed efficiency when fed a common diet. Second parity cows lost more body weight than first parity cows and had greater feed efficiency in early lactation as a result; these responses were unaffected by breed. In this study, in early lactation, Holstein and Jersey cows did not have different feed efficiencies.

1. Genome assembly of the rumen microbial community and identification of rumen virome interactions. Better definition of the ruminant microbiome was needed to improve overall annotation of genes, genetic variation, epigenetic variation, and other sequence motifs that affect phenotype expression. In a large international collaboration between scientists from the United Kingdom (Roslin Institute) and the United States (USDA ARS, Pacific Biosciences, Phase Genomics, and the National Institute of Health), ARS researchers in Madison, Wisconsin, and Beltsville, Maryland, assembled 103 medium-quality draft genomes from bacteria and archaea (methanogenic microbes) in the cattle rumen using cutting-edge software that they developed and the latest long-read sequencing data. They also identified 188 novel host-viral interactions that provided the first high-resolution glimpse of the activity of viruses in the cattle rumen. The new assembly methods pioneered by ARS scientists allowed identification of 94 antimicrobial-resistance genes that may confer antibiotic resistance to rumen bacteria and improve animal health. The analysis of this dataset was published in Genome Biology as part of a special issue on the microbiome. Already, several research groups have used this method to identify potential vectors for antimicrobial-resistance gene alleles in human medicine and the software that implements this method averages two unique, weekly visitors since publication.

2. New water-soluble starch method improves information on animal feeds. Animal nutritionists serving the livestock industries rely on commercial analytical laboratories to provide them with accurate feed analyses in which the measured components have nutritional relevance. Current methods of analysis were known to have problems with specific corn-derived feeds where analyses for water-soluble carbohydrates (WSC) and starch, when summed, contributed to unrealistically high values substantially exceeding 100% of dry matter. ARS researchers at Madison, Wisconsin, developed an improved method that resolved the problem where one of the measured components was inaccurately quantified. This allowed for more accurate formulation of dairy cattle rations, thus ensuring better nutrition. This improved method was shared with commercial laboratories, thus making it available to industry and to field nutritionists. This research provided animal agriculture with an assay to accurately determine the nutritional quality of feeds for animals and more efficient use of resources.

3. Dosing microbial-enriched ruminal inoculum into young calves altered ruminal fermentation. Ruminant microbial community consists of members from three domains of life such as methanogenic archaea, bacteria, and members of eukaryota: protists and fungi. The ruminal protists have been relatively underexplored compared to the ruminal bacteria, however it is known that the protists contribute directly or indirectly to increased methane output, reduced nitrogen use efficiency, and reduced feed efficiency. ARS scientists in Madison, Wisconsin, explored the establishment of ruminal protists in dairy calves through direct, early-life inoculation with protist- or bacteria-enriched ruminal inoculum. During continual ruminal inoculation, microbial inoculum composition altered the ruminal environment, without affecting calf performance. The protist community was not maintained and was dissimilar from a typical adult protozoal population. This study highlighted some of the challenges in directing the developing rumen microbial environment and bacterial community. Under these conditions, the pre-weaned calf ruminal environment was not ideal for establishing rumen microbiota from adult cows. However, the responses to continued ruminal inoculation will provide researchers with valuable information for when attempting to direct the dairy calf ruminal environment toward profitable and efficient phenotypes.

Review Publications
Gelsinger, S.L., Coblentz, W.K., Zanton, G.I., Ogden, R.K., Akins, M.S. 2020. Physiological effects of starter-induced ruminal acidosis in calves before, during, and after weaning. Journal of Dairy Science. 103(3):2762-2772.
Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9.
Liu, R., Yee Low, W., Tearle, R., Koren, S., Ghurye, J., Rhie, A., Phillippy, A.M., Rosen, B.D., Bickhart, D.M., Smith, T.P., Hiendleder, S., Williams, J.L. 2019. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. BMC Genomics. 20:1000.
Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T., Hardy, T., Hackett, P., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P. 2020. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience. 9(4):1-9.
Sbardellati, D., Fischer, A., Cox, M.S., Li, W., Kalscheur, K., Suen, G. 2020. The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of Dairy Science. 103(4):3636–3647.
Van Soest, P.J., Robertson, J.B., Hall, M., Barry, M.C. 2020. Klason lignin is a nutritionally heterogeneous fraction unsuitable for the prediction of forage neutral-detergent fibre digestibility in ruminants. British Journal of Nutrition. 1-8.