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United States Department of Agriculture

Agricultural Research Service



2011 Annual Report

1a. Objectives (from AD-416)
The overall objectives of the research project are to apply modern genomic tools to the identification and characterization of genetic pathways, physiological mechanisms, and microbial-host interactions that modulate nutrient uptake, partitioning, and loss in cattle. The specific objectives include development of resources for identification of selectable markers of nutrient efficiency, identification and characterization of genetic pathways and/or genomic regions influencing critical regulatory pathways of nutrient efficiency and transport, and development of intervention strategies to enhance nutrient uptake and partitioning in cattle.

1b. Approach (from AD-416)
To identify and characterize factors affecting nutrient use efficiency in cattle, resources will be developed including a phenotypic database of dairy efficiency and corresponding DNA and tissue collections, methods for live animal intestinal tissue collection suitable for gene expression studies, and sub-populations of dairy cattle to investigate inflammation and nutrient use interactions. Novel DNA sequencing technology will also be evaluated for its utility in characterizing changes in rumen microbial populations during rumen development. Transcript profiling techniques including microarray and quantitative real-time PCR will be used to establish molecular markers of proliferation, development and differentiation of the bovine gastrointestinal tract, and to identify metabolic and hormone pathways controlling nutrient metabolism in the ruminant gastrointestinal tract. Finally, two dietary strategies that potentially affect the rumen microbial population and production efficiency will be studied for their effects on nutrient use efficiency in cattle.

3. Progress Report
A study was initiated to examine the use of a hormone produced in the gut called GLP-2 to improve nutrient absorption and reverse/prevent damage of the gut from calf scours using a parasite infection model. The hormone has been used as a therapy to improve gut healing in human patients with Crohn’s disease and to reduce gut injury from chemotherapy-induced inflammation of the gut. Progress was made (Objective 2) to study cell growth regulation pathways induced by volatile fatty acids (VFA), a primary energy source for cattle produced by microbes in the rumen. We demonstrated a role of VFA in modulating cellular functions in development, cell division, and programmed cell death. We were first to show that VFA induce changes in gene expression involving 2 gene regulatory machineries--microRNA and histone acetylation. At the request of the Office of National Programs, we studied whether the Brown Marmorated Stink Bug, an invasive Asian species, could taint milk flavor if consumed by the lactating cow. We dosed the primary odor-causing compound into the rumen of dairy cows for 3 days at doses that represent the highest potential delivery under the current worst-case infestation scenario. The compound was undetectable in milk, feces, and rumen fluid during the 7 days of sampling after dosing, suggesting that rumen microbes quickly bioremediate the potential milk contaminant. Relative to Objective 2, biopsy approaches were adapted to enable repeated sampling from not only rumen, but also intestinal epithelia to support gene expression analyses of nutrient delivery. Using serial samples collected from cows, we were able to observe for the first time, expression of genes with defined regulatory roles in other stratified squamous epithelial tissues. Multiple experiments using this biopsy approach are underway. Negative impacts of endophyte-infected fescue are well established in the southern U.S. To determine impacts of feeding (or pasturing) dry cattle on infected fescue on subsequent nutrient use efficiency and lactation performance, rations containing either endophyte-free or endophyte-infected seed were fed to late-lactating, dry, and early lactation cows. Mammary gland biopsies and blood samples were collected in addition to standard production measures. Analyses are pending. Liver and muscle tissue nutrient use impact whole body nutrient use efficiency. Relative to Objective 2, growth and differentiation of function in these tissues were assessed using microarray and Whole Transcriptome Shotgun Sequencing approaches to assess changes in gene expression related to changes is dietary macronutrients (propionate, casein, and starch). An experiment was initiated to understand how zinc methionine affects the rumen microbial ecosystem of dairy cows. Projects to dissect dynamics of the rumen microbiota in response to sodium butyrate infusion and to understand temporal sequences of microbial establishment in the developing rumen of calves were completed. Our preliminary findings from metagenomic studies support the idea that intimate interplays between the bovine host and its microbiota play an important role in defining nutrient utilization efficiency.

4. Accomplishments
1. Characterized a feed efficiency trait in lactating dairy cattle, called residual feed intake (RFI). The trait is used to select beef cattle that are more efficient at conversion of feed to gain and produce less methane (a greenhouse gas) during digestion. We found that RFI is heritable in dairy cattle and repeatable within cows over multiple lactations. Consistent with beef cattle, low-RFI (efficient) cows consumed 17% less feed than high-RFI (inefficient) cows, with no differences in energy-corrected milk yield or body weight. Relative to inefficient cows, efficient cows spent less time feeding and ate at a slower rate, which are thought to reduce energy expenditure, contribute to increases in digestibility of feed, and ultimately increase the efficiency of feed conversion to milk. The results suggest that RFI is a trait to consider for multi-trait genetic selection of dairy cattle to reduce feed costs and the environmental impacts of dairy production.

2. Improved understanding of temporal sequences of microbial establishment in the rumen of pre-ruminant calves. Using 2 molecular approaches and pyrosequencing, 15 bacterial phyla in the microbiota of pre-ruminant calves were identified and their relative abundance characterized during rumen development. A total of 170 bacterial genera were identified, while the core microbiome of pre-ruminant calves included 45 genera. Rumen development seemingly had a significant impact on microbial diversity. Results also suggested that rumen microbial communities of pre-ruminant calves maintain a stable function and metabolic potentials while their phylogenetic composition fluctuates greatly. The presence of all major types of rumen microorganisms suggests that the rumen of pre-ruminant calves may not be rudimentary. Our results provide insight into rumen microbiota dynamics and will facilitate efforts to formulate optimal early-weaning strategies.

3. Developed high-resolution maps of sequences in the bovine genome involved in epigenetic regulation of gene expression by dietary volatile fatty acids (VFA). In collaboration with the Lieber Institute for Brain Development, Johns Hopkins University, we studied the epigenomic structure of bovine cells affected by butyrate. Chromatin modification is an important mechanism regulating expression of genes in the genome, which can influence cell function and development. We revealed that VFA, especially butyrate, participate in cell metabolism both as nutrients and as regulators of histone modification, thereby regulating the ‘epigenomic code.’ We completed a genome-wide, high-resolution map of ‘normal’ histone acetylation versus ‘acetylated’ histone 3 induced by butyrate in bovine cells. The maps of these sites allow us to identify the precise sequence context of histone modification and histone modification target sites in the bovine genome, and gain insight into the interaction of dietary nutrients and their effects on the genome.

Review Publications
Do Amaral, B., Connor, E.E., Tao, S., Hayen, J., Bubolz, J., Dahl, G. 2011. Heat Stress Abatement During the Dry Period Influences Metabolic Gene Expression and Improves Immune Status in the Transition Period of Dairy Cows. Journal of Dairy Science. 94:86-96.

Hill, R.A., Welsh, T.H., Poulos, S.P., Gabler, N.K., Connor, E.E. 2011. Growth and development symposium: Intestinal development and growth. Journal of Animal Science. 89:833-834.

Kadegowda, A.K., Connor, E.E., Teter, B.B., Sampugna, J., Delmonte, P., Piperova, L.S., Erdman, R.A. 2010. Dietary trans fatty acid isomers differ in their effects on mammary lipid metabolism as well as lipogenic gene expression in lactating mice. Journal of Nutrition. 140:919-924.

Connor, E.E., Baldwin, R.L., Capuco, A.V., Clover, C.M., Ellis, S.E., Sciabica, K.E. 2010. The glucagon-like peptide 2 pathway may mediate growth and development of the bovine gastrointestinal tract. Journal of Dairy Science. 93:5167-5178.

Li, C., Li, R.W., Elsasser, T.H. 2010. Alpha-Tocopherol modulates transcriptional activities that affect essential biological processes in Bovine Cells. Gene Regulation and Systems Biology. 4:109-124.

Li, C., Li, R.W., Elsasser, T.H. 2010. MicroRNA (miRNA) expression is regulated by butyrate induced epigenetic modulation of gene expression in bovine cells. Genetics and Epigenetics. 3:23-32.

Sparks, M., Huang, Y., Baldwin, R.L., Connor, E.E., Li, C., Sonstegard, T.S., Schroeder, S.G., Li, R.W. 2011. Metagenomics detects functional shifts in the bovine rumen microbiota in response to propionate intake. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 165-183.

Li, C. 2011. Specific cell cycle synchronization with butyrate and cell cycle analysis. In: Banfalvi, G., editor. Methods in Molecular Biology, Cell Cycle Synchronization: Methods and Protocols. New York NY: Humana Press. p. 125-136.

Li, R.W., Sparks, M., Connor, E.E. 2011. Dynamics of the rumen microbiota. In: Li, R.W., editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 135-164.

Sparks, M., Li, R.W. 2011. Towards a more complete metagenomics toolkit. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 33-45.

Huang, Y., Li, W., Perkins, D., Li, R.W. 2011. Comparison of de novo short read assemblers on metagenomic data. In: Li, R.W. editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 107-120.

Last Modified: 05/23/2017
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