Microbiome of the upper nasal cavity of beef calves prior to weaning

Authors: McDaneld, Tara; Kuehn, Larry; Keele, John

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2019
Publication Date: 4/10/2019
Citation: McDaneld, T.G., Kuehn, L.A., Keele, J.W. 2019. Microbiome of the upper nasal cavity of beef calves prior to weaning. Journal of Animal Science. 97:2368–2375. https://doi.org/10.1093/jas/skz119.
DOI: https://doi.org/10.1093/jas/skz119

Interpretive Summary: Disease incidence is intimately associated with an animal’s commensal bacteria populations, as the microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. In addition, bacterial pathogens affect the immune system and appear to play an integral role in the overall incidence of diseases including bovine respiratory disease complex (BRDC), so an understanding of the interaction of the animal’s resident respiratory pathogens (metagenome) including microbial agents in the upper nasal cavity may help us to understand the impact of these pathogens on incidence of BRDC in cattle. For this research the overall goal was to characterize the bacterial populations associated with calves in three herds at the US Meat Animal Research Center (USMARC) from early age through time periods relevant to weaning. To determine the metagenome from the upper respiratory tract of calves from these three herds, nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 70 days of age), preconditioning (approximately 140 days of age), and weaning (approximately 160 days of age) in 2015 and 2016. Overall, bacterial profiles differed across the two years evaluated and across sampling time points for each herd. Analysis of specific respiratory pathogens prior to weaning will provide important information, which will present a clearer picture of the relationships of profiles in animals that develop BRDC or not. Therefore, evaluation of the animal’s resident bacterial populations in the upper nasal cavity may help us to understand the impact of the metagenome on incidence of BRDC in cattle.

Technical Abstract: Disease incidence is intimately associated with an animal’s commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. An understanding of the animal’s resident respiratory pathogens, in the upper nasal cavity prior to weaning, may help us to understand the impact of these pathogens on incidence of respiratory disease. For this research, the overall goal was to characterize bacterial populations associated with calves at an early age and through time periods prior to weaning in 3 herds at the U.S. Meat Animal Research Center. Nasal swabs from the upper nasal cavity were collected at initial vaccination (approximately 40 d of age), preconditioning (approximately 130 d of age), and weaning (approximately 150 d of age) in 2015 and 2016. DNA was extracted from nasal swabs and combined into 2 pools of 10 animals for each sampling time point, in each herd, for a total of 6 pools at each sampling time point and 18 pools for all sampling time points within each year. To evaluate and compare the microbiome of each pooled sample, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Alpha and beta diversity were also measured. Overall, microbial communities were different between combinations of sampling year, herd location, and sampling time prior to weaning as shown by beta diversity. Analysis of these specific respiratory pathogens prior to weaning will present a clearer picture of the distribution of microbial populations in animals prior to weaning and not exhibiting clinical signs of respiratory disease. Therefore, evaluation of the animal’s resident bacterial populations in the upper nasal cavity during different phases of the beef production system may help us to understand the impact of the microbiome on incidence of respiratory disease in cattle.