Location: Cell Wall Biology and Utilization Research
Project Number: 5090-31000-028-000-D
Project Type: In-House Appropriated
Start Date: Sep 1, 2022
End Date: Aug 31, 2027
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.
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 develop a procedure that lyses bacteria without solubilizing feed protein to allow application of dye binding assays to determine microbial true protein in ruminal or in vitro fermentation samples. Results will be evaluated for solubilization of protein from feed and microbial sources relative to total N content of untreated samples. 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.