Location: Cell Wall Biology and Utilization Research
2024 Annual Report
Objectives
Objective 1: Evaluate digestive tract function and identify gastrointestinal microorganism effects on nutrient digestibility, milk production capacity, nutrient use efficiency, and health in dairy cattle.
Sub-objective 1.A: Characterize and develop tools to evaluate the microorganisms present in the digestive tract of dairy cattle and evaluate effects of nutritional or other strategies on composition of microorganisms present and effects on performance and nutrient utilization efficiency.
Sub-objective 1.B: Evaluate functional microbiology, gastrointestinal function and digesta passage, and dietary composition effects on nutrient digestibility for increased performance, nutrient use efficiency, and health.
Objective 2: Characterize dairy cattle physiological factors contributing towards improved milk production capacity, nutrient use efficiency, and health.
Sub-objective 2.A: Utilize dairy cattle transcriptomics to inform the connections between the genotype and phenotype and the interaction of genotype and phenotype to enable improved milk production capacity, productive efficiency, milk quality, and health.
Sub-objective 2.B: Develop an understanding of the metabolic or physiological functions that determine production potential of partitioning of nutrients toward milk and away from manure and greenhouse gas emissions.
Approach
For sub-objective 1.A, we will characterize the rumen metagenomic community. We will collect rumen solids and liquids from cannulated Holstein cows and cannulated Jersey cows and sequence to a depth of 200 million paired-end reads using a circular consensus sequence protocol. These datasets will represent the finest resolution microbial references for the Holstein and Jersey breeds of cattle. We will also evaluate vitamin B12 status and behavior in heifers reared grazing on pasture or fed a total mixed ration in the barn.
For Sub-objective 1.B, we will evaluate if rumen microbial efficiency of microbial protein production is associated with the ratio of degradable protein to degradable carbohydrate through meta-analysis. We will also assess the fit of a two-pool three-exponential rate liquid passage kinetics model in vitro using two fiber sources. The fit of the in vitro data to a one-pool (free liquid) or two-pool (liquid as free liquid and associated with solids) liquid passage model will be determined. The difference between diets in in vivo rate of liquid passage and in vitro behavior of marker between liquid and solid fractions will be compared. This will provide insights related to passage of liquid-associated nutrients from the rumen as affected by physical form of the diet. In vitro rumen degradation of feedstuff protein using intrinsically labelled 15N will also be determined.
For Sub-objective 2.A, we will identify transcriptome biomarkers and adaptive transcriptome changes in dairy cows in response to different diets and during different development and lactation stages. Whole blood and milk samples will be collected prior to the administration of dietary treatments and after the cows have been adapted to the dietary treatments for downstream transcriptome biomarker analysis. We will also determine if dairy cattle with compromised ruminal health or gut barrier disfunction and healthy dairy cattle have distinct gastrointestinal tissue transcriptome and metatranscriptome profiles. Dairy bull calves will be offered calf starter diets of increased (acidosis) or typical (healthy) fermentability. Total RNA will be extracted from tissue samples, sequenced, and any reads unmapped to the cattle reference will be considered microbial and used for downstream microbial community analysis including potential microbial function analysis.
For Sub-objective 2.B, we will evaluate if milk component production is associated with greenhouse gas emissions and changes in energetic efficiency of use of absorbed nutrients through meta-analysis, which will provide a more complete description of measurable outcomes of cow performance and their relationship to greenhouse gas emissions and efficiency of diet utilization. Additionally, we will evaluate whether lactation performance, nitrogen and feed efficiency, and manure characteristics will be differentially affected by diet provided to Holstein and Jersey cows.
Progress Report
Objective 1. Sub-objective 1.A: To develop high-resolution microbial references and characterize the ruminal metagenomic community, ruminal samples have been collected from Holstein and Jersey cows, processed for maximum high molecular weight DNA extraction, and sequenced. After initial quality control steps, this resulted in an observed average sequence length (N50) of 13,306, for the reads from Holstein cows, and an average N50 of 2,377 for the Jersey reads. These higher N50’s will allow easier assembly of the rumen microbial genomes present in these samples. Initial results from microbial classification indicate strong differences in microbial populations between Jersey and Holstein cattle. To interrogate this difference further, we will continue collecting ruminal samples for further sequencing and analysis to not only supplement our current data set but to also identify mobile genetic elements in the microbial community that could transfer genetic material across microbial species. Additionally, a study to evaluate vitamin B12 status and behavior of dairy heifers raised on pasture or in confinement has begun and had the first summer of sampling completed. Analysis of the initial year’s hair cortisol samples and behavior data have been completed. Year 2 sampling of blood, hair, and performing behavior observations has begun.
Objective 1. Sub-objective 1.B: Animal research on ruminal liquid passage kinetics in the two-pool (liquid and solids) system was discontinued based on analysis of a past study which showed no difference from the traditional approach to estimate liquid passage rate. The method currently available for separating liquid and solids has potential to infuse liquid marker into the solids and press liquid marker from the solids, which could have been a basis for the lack of difference between the two approaches.
Objective 2. Sub-objective 2.A: 1. A dairy calf study was completed to evaluate the impact of diet-induced, early- life sub-acute ruminal acidosis (SARA) on health and microbiome establishment. Calves were fed 2 different dietary treatments intended to induce or blunt SARA from birth to weaning after which liver biopsies, ruminal fluid, and blood samples were collected for RNA sequencing. The blood and liver samples are being analyzed to identify blood-based microbial biomarkers that can aid the detection of SARA which could help identify early detection biomarkers of SARA and help design effective, feed-based management tools to prevent it on farms. A bioinformatic workflow that enables identification of antimicrobial resistance genes (ARG) from microbial species attached to the epithelial layer of the cattle gastrointestinal (GI) tract has been designed and validated. Specifically, this workflow unmasks the attached epithelial microbial population by filtering out the cattle RNA transcripts from total RNA sequencing data gathered from cattle GI tract. The filtered reads were further enriched for microbial antibiotic resistance genes using curated ARGs. The bioinformatic workflow can be used to further assess single nucleotide polymorphism in the ARGs identified at various GI locations. The rumen epithelial transcriptome analysis from calves artificially inoculated with rumen microbes has been completed. The inoculum treatments were prepared from rumen contents collected from canulated lactating cows and were processed into bacterial- or protozoal-enriched microbial fractions. The results of the study indicated that inoculation of differentially processed rumen microbes influences the rumen epithelial transcriptome and the metatranscriptome of its microbial communities. Single-cell RNA sequencing is a powerful new technique that enables the comparison of the transcriptomes of individual cells within a sample containing a diverse population of cells. A single-cell RNA sequencing experiment has been conducted from Peyer’s patch and mesenteric lymph node tissue from the jejunum and ileum of one-week old calves. From the initial data analysis, the results indicate unique transcriptome profiles for cell clusters from each location in the small intestine.
Objective 2. Sub-objective 2B: Through meta-analysis, it was determined that Holstein dairy cattle respond to supplemental rumen protected methionine with increased milk fat and protein production. The transition period occurs 21 days prior to calving through 21 days after calving and is a dynamic and highly stressful management period in the lifecycle of the cow. Studies with Jersey cows in the transition period and whether a productive response to supplemental methionine during the transition period occurs is unknown. To address this deficiency a study evaluating the effects of supplementing rumen protected methionine to Holstein and Jersey cows during the transition period has begun. Results from this study will assist nutritionists in targeting recommendations for herds of different breeds.
Accomplishments
1. Rumen protected methionine supplementation during the transition period improves dairy cow milk productive performance. The transition period, defined as three weeks before and after calving, is a very important time in the life of a cow that has multiple impacts on the health and productivity of the dam and calf. Methionine is an amino acid that is often considered limiting for milk protein productivity, but also has many physiological functions beyond protein synthesis. In collaboration with a researcher from the University of Wisconsin-Madison, an ARS scientist in Madison, Wisconsin, reviewed and synthesized the literature on methionine supplementation to transition dairy cows by meta-analysis. Through this analysis, supplemental rumen protected methionine (sRPMet) was determined to increase milk fat and protein production. Additionally, the response to supplemental rumen protected methionine declined as lactation progressed indicating that feeding before and after calving increased production beyond what would be expected by providing sRPMet in established lactation alone. These results are important in guiding dairy farmers and their nutritionists to precisely target nutrient supplementation to dairy cows for capturing the most efficient productive response and could lead to reduced protein/nitrogen in dairy diets and a proportional loading of nitrogen in manure and the environment.
Review Publications
Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W., Pausch, H., Demyda-Peyras, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. 2023. The bovine pangenome consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biology. 24. Article 139. https://doi.org/10.1186/s13059-023-02975-0.
Fuller, T.D., Bickhart, D.M., Koch, L.M., Kucek, L.K., Ali, S., Mangelson, H., Monteros, M.J., Hernandez, T., Smith, T.P., Riday, H., Sullivan, M.L. 2023. A reference assembly for the legume cover crop hairy vetch (Vicia villosa). GigaByte. https://doi.org/10.46471/gigabyte.98.
Hall, M., Mertens, D.R. 2023. Comparison of alternative neutral detergent fiber methods to the AOAC definitive method. Journal of Dairy Science. 106(8):5364-5378. https://doi.org/10.3168/jds.2022-22847.
Guduk, E., Hall, M., Zanton, G.I., Steinberger, A.J., Weimer, P.J., Suen, G., Weigel, K.A. 2023. Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen degradable protein. Frontiers in Microbiomes. 2. Article 1204988. https://doi.org/10.3389/frmbi.2023.1204988.
Kearney, C.C., Ball, R., Hall, M. 2024. Effects of altering diet carbohydrate profile and physical form on zoo-housed giraffe Giraffa camelopardalis reticulata. Journal of Animal Physiology and Animal Nutrition. https://doi.org/10.1111/jpn.13957.
Caputo, M., Li, W., Kendall, S., Larsen, A., Weigel, K., White, H. 2023. Liver and muscle transcriptomes differ in mid-lactation cows divergent in feed efficiency in the presence or absence of supplemental rumen-protected choline. Metabolites. https://doi.org/10.3390/metabo13091023.
Erickson, M., Reinhardt, L.A., Svaren, L.M., Sullivan, M.L., Zanton, G.I., Wattiaux, M. 2024. Crude protein oscillation in diets adequate and deficient in metabolizable protein: effects on nutrient digestibility, nitrogen balance, plasma amino acids, and greenhouse gas emissions. Journal of Dairy Science. https://doi.org/10.3168/jds.2023-24150.