<p dir="ltr">ABSTRACT</p><p dir="ltr">Bovine Respiratory Disease (BRD) poses a significant challenge in the dairy and beef industry, contributing to high mortality, morbidity, and economic costs. Extensive research has aimed to enhance BRD diagnosis, focusing on various factors such as predisposition, environment, and epidemiology. While diverse methods have been developed for BRD detection, including clinical signs, behavioral changes, lung consolidation assessment via ultrasonography, and molecular techniques for microbiome analysis, accurate diagnosis remain inconsistent. Notably, many studies lack exploration of microbial interactions (fungi, viruses, and bacteria) within BRD-affected animals compared to healthy ones. Moreover, the impact of age, disease, and antibiotic treatment on the microbiome community remains understudied. Thus, additional analysis is crucial to understand the relationships between these factors and BRD development. This dissertation is divided into two parts, each addressing specific conditions. The first part focuses on characterizing the nasopharyngeal (NP) microbiome of dairy calves, pre-weaned and post-transported, and those diagnosed with BRD within the first two weeks of life. The objective is to identify NP microbiome changes as indicators of disease development, considering antibiotic treatment effects on NP alpha and beta diversity. The second part delves into characterizing the fungal and bacterial nasal cavity among BRD-affected and healthy cattle within the same pen. This section, presented in three chapters, explores the bovine nasal mycobiome in beef cattle, as well as the nasal microbiome in both dairy and beef cattle. The overarching goals of these studies are to evaluate differences in the nasal mycobiome or microbiome community between BRD-affected and healthy cattle, focusing on alpha, beta, and community compositions as potential disease indicators. Additionally, the aim is to determine if BRD-affected cattle exhibit higher abundance of BRD-pathobionts (fungi and bacteria) in the nasal cavity compared to healthy pen-mates. In conclusion, findings from this research emphasize the importance of incorporating both mycobiome and microbiome analyses in understanding BRD development. Future studies should consider geographical influences on nasal microbiome structure, highlighting the need for separate investigations in dairy and beef calves due to breed variations. Ultimately, studying mycobiome and microbiome ecology offers insights into microbial transitions from commensal to pathogenic farms in the bovine upper respiratory tract, supporting advancements in BRD prevention or mitigation strategies.</p>