Characterization of Microbiomes Related to Respiratory Disease in Cattle

Bovine respiratory disease complex (BRDC) is the largest disease-related issue for the beef cattle industry in the U.S., estimated to cause 75% of morbidity in beef cattle feedlots.   Despite decades of research, incidence of BRDC has not been sufficiently reduced at the feedlot level and causes 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, including examination of microbiomes associated with BRDC.  A general overview of this program, followed by a discussion of pertinent microbial environments and results bearing on the selection of sequencing platforms (MiSeq and PacBio) and PCR primers, will be presented.  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.