Characterizing the Microbiome of Beef Cattle to Identify Risk Factors That Affect Respiratory Health

Project Title

Characterizing the Microbiome of Beef Cattle to Identify Risk Factors That Affect Respiratory Health


Trevor Alexander, PhD and Edouard Timsit D.V.M.

Edouard Timsit D.V.M. (University of Calgary); Trevor Alexander, PhD, Tim McAllister Ph.D., Dallas Thomas Ph.D., Oscar Lopez Campos Ph.D., Devin Holman Ph.D., (Agriculture Agri-Food Canada); Kim Stanford Ph.D., (Alberta Agriculture); Yanyun Huang Ph.D. (Prairie Diagnostic Services); Craig Dorin D.V.M. (Veterinary Agri Health Services)

Scientific Journals

Status Project Code
Completed April, 2023 AMR.10.17


Bovine respiratory disease (BRD) is one of the most significant health problems in beef cattle, resulting in considerable economic losses due to mortalities, cost of treatment, reduced feed efficiency, and lower carcass quality.  In beef production, antimicrobials are used for the prevention and treatment of BRD.  However, there are public and scientific concerns regarding antimicrobial use in livestock and resistance in BRD-associated bacterial pathogens may be increasing. It is therefore important to investigate alternative strategies to mitigate BRD.  Recently, research in animals has shown that the respiratory microbiota (collective microbes within a community) has an important role in maintaining health and that a disruption of the microbiota can lead to colonization and infection by pathogens. In cattle, the respiratory bacteria have been observed to be dynamic, but limited information exists on changes that occur from farm to feedlot. The purpose of this project was to characterize the respiratory microbiota of calves, in order to identify factors that affect BRD susceptibility.


  • Characterize the bovine nasopharyngeal microbiota from birth to weaning and define animal, management, and environmental elements that influence the nasopharyngeal microbiota of and how those elements correlate with animal health.
  • Determine how bacterial communities change along the respiratory tract and how they relate to the development of BRD.

What They Did

To achieve the objectives, six studies were conducted that incorporated DNA sequencing to characterize the respiratory microbiota in cattle. 

In Study 1, a cohort of cattle were sampled by deep nasal swabs (DNS) to determine how management and environmental aspects shape the respiratory tract microbiota in calves entering feedlots. In Study 2, DNS were collected from calves at birth, and then at various time points until weaning, to evaluate the composition of bacteria during calf development and when the respiratory microbiota stabilizes. To further our understanding of the microbiota colonizing cattle, bacteria were characterized in samples collected from 17 distinct locations of the upper and lower respiratory tracts of healthy calves in Study 3. 

In a fourth study, the upper and lower respiratory tract were also investigated across time, in cattle diagnosed with BRD, to identify changes in bacteria that occur throughout BRD progression. Finally, how on-farm preconditioning affects the respiratory microbiota was studied in cattle transported to feedlots.  In Study 5, preconditioned cattle were mixed at varying rates with auction-market cattle to evaluate the impact of comingling on the respiratory microbiota, while in Study 6, preconditioned and nonconditioned calves were mixed with auction market cattle after 12 hours of transportation to a feedlot.

What they learned

When the DNS collected from cattle at entry to multiple feedlots across Alberta were evaluated, there were no clear differences in bacteria and viruses of animals that later developed BRD, compared to those that remained healthy throughout feedlot placement.  Despite this, it was shown that certain bacterial and viral taxa associated with BRD were present in cattle at feedlot arrival, indicating that colonization and proliferation of these microorganisms can take place prior to feedlot placement. Therefore, preconditioning and other strategies to reduce stress can help to maintain a healthy microbial balance in the respiratory tract and reduce the risk of BRD.

Exploring this further, they found that on-farm preconditioning programs (including vaccination against bacterial and viral BRD pathogens) could enhance respiratory health. The BRD incidence in preconditioned calves was not affected by comingling with auction market calves, but the incidence of BRD was lower in preconditioned animals compared to auction-derived calves. 

Preconditioned calves had also reduced stress responses resulting from transportation and feedlot placement compared to nonconditioned calves. Preconditioned calves also carried fewer BRD-bacteria. Improved vaccines that have better efficacy  may enhance the benefits of preconditioning programs further.

This team also investigated the respiratory microbiota in calves from birth to weaning. They found that some commensal (naturally occurring) bacteria in DNS were observed to inhibit BRD pathogens.  However, these beneficial commensal bacteria decreased in abundance from birth to weaning, while the BRD-associated bacteria became more abundant. Therefore, finding ways to deliver these commensal bacteria as probiotics to young calves on-farm may enhance respiratory health prior to weaning and feedlot transportation.  This concept was supported by a proof-of-concept study, that showed that the intranasal application of probiotic bacteria could influence the respiratory microbiota of calves in the long-term.  It was determined that the application of probiotic bacteria should be targeted to the nasopharynx, as bacteria in this part of the upper respiratory tract were most similar to those of the lungs, where BRD infection occurs.

What it Means

This project provided a comprehensive overview of the respiratory microbiota in calves and factors that affected it. This team used sequencing-based technologies to identify bacteria and viruses in the respiratory tract, characterize how bacteria evolve during calf growth and how those bacteria respond to management stressors.  It was shown that BRD and calf stress can be reduced by utilizing currently available vaccines and management strategies in preconditioning programs.  However, improving vaccine management and practices on-farm would likely further enhance the effectiveness of preconditioning programs further. In addition, based on observed relationships between bacterial commensals and pathogens in the upper respiratory tract, it was proposed that probiotics may be useful in mitigating BRD in the future.