Date of Graduation

12-2020

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Animal Science (PhD)

Degree Level

Graduate

Department

Animal Science

Advisor/Mentor

Jiangchao Zhao

Committee Member

Beth Kegley

Second Committee Member

Jung Ae Lee-Bartlett

Third Committee Member

Jeremy G. Powell

Keywords

bovine respiratory disease, cattle, microbiome, pathogens, respiratory microbiota, spatial dynamics

Abstract

Bovine respiratory disease (BRD) is the most common and costly disease in the beef cattle industry, leading to high morbidity, mortality and huge economic loss. Despite the recent advances in vaccination and antimicrobial techniques, no significant health-improved outcomes have developed. Due to a deep investigation of the microbiome, respiratory microbiotas are known to have important roles for host health and disease. However, BRD specific pathogens have not yet been identified since they are found in both healthy and diseased animals. A systemic and comprehensive study of the biogeography of the bovine respiratory microbiome and its relationship with BRD is lacking and urgently needed. In this dissertation, we characterized the biogeography of the bovine respiratory microbiome from a total of 222 samples and identified the microbial composition of the nostrils, nasopharynx and lungs. Signature microbiota for each niche were identified (Chapter III). Shared bacteria among the three niches were observed, and a strong correlation between adjacent sampling niches was found. Next, using a random forest model (Chapter IV), high accuracies of the nasal, nasopharyngeal and lung microbiomes to predict and diagnose BRD were found. A set of bacterial features were identified. A significantly temporal dynamic of the respiratory microbiome was found from feedlot arrival to the onset of BRD, with consistent increases in the abundance of BRD pathogens and consistent decreases of the commensal microbiota. Finally, the spatial microbial movement within the bovine respiratory tract associated with BRD status was clarified (Chapter V). A larger proportion of the lung microbiota was found to be derived from the upper airway community in BRD calves compared to healthy calves, and pathogens in BRD lungs could be predicted by using their abundances in the BRD upper airway. Complex interactions among commensal microbiota were found in healthy calves, while dysbiosis of the microbial community as well as increased pathogen interactions in the airway were found in BRD calves. All our discoveries from the first (test) trial were validated in the second (validation) animal trial. In conclusion, this comprehensive study further advanced our understanding of the relationship between the respiratory microbiome and BRD. Additionally, nasal swabbing was found as an innovative approach to be used for BRD research. It provides a new research direction into airway disease research and is capable of providing more advanced microbial therapies for bovine respiratory disease.

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