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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics, Breeding, & Animal Health

Title: Characterization of microbiomes related to respiratory disease in cattle

Authors
item Smith, Timothy
item Kim, Min Seok
item Myer, Phillip
item McDaneld, Tara
item Kuehn, Larry
item Clawson, Michael
item Harhay, Dayna
item Harhay, Gregory

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 28, 2013
Publication Date: January 11, 2014
Citation: Smith, T.P., Kim, M.S., Myer, P.R., McDaneld, T.G., Kuehn, L.A., Clawson, M.L., Harhay, D.M., Harhay, G.P. 2014. Characterization of microbiomes related to respiratory disease in cattle [Abstract]. Proceedings of the Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster W759.

Technical Abstract: Respiratory disease is the single largest disease-related issue for the beef cattle industry in the United States, estimated to be responsible for up to 75% of morbidity in beef cattle feedlots. Despite decades of research into this problem, incidence of bovine respiratory disease complex (BRDC) has not been sufficiently reduced at the feedlot level and continues to be the cause of approximately 25-30% of the mortality in beef cattle feeding and stocker operations. Moreover, the use of antibiotics in cattle production to combat BRDC is coming under increased pressure as antibiotic resistance in human pathogens has become an emerging issue. The U.S. Meat Animal Research Center (USMARC) has a comprehensive program to investigate the causes, effects, and treatments of BRDC from both the host genetics and microbial sides of the problem. As part of this effort, we have begun to examine microbiomes associated with the animals and environments contributing to BRDC. A brief, general overview of this program will be presented, followed by a discussion of pertinent microbial environments and results bearing on the selection of sequencing platforms and PCR primers. Comparison between different variable regions of the 16S rRNA gene for diversity studies using the MiSeq and PacBio platforms indicates that the MiSeq platform provides deeper sequencing for a given cost. However, the relatively short read length limits the number of variable regions examined and reduces the accuracy of classification compared to the near full-length sequence possible with the PacBio platform. The profiles of 16S rRNA gene sequences in the bovine respiratory tract indicate that the microbiome is generally dominated by Mannheimia, Moraxella, Pasteurella, and Mycoplasma, with some symptomatic animals having high percentages of either Mannheimia or Mycoplasma in samples from their nasopharyngeal or anterior nares. The goals of the metagenome aspects of the USMARC BRDC project are to correlate microbial populations prior to and after infection, to identify potential predictors of disease and/or suggest more effective control strategies that are less dependent on unguided mass medication regimes.

Last Modified: 10/19/2014
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