Abstract
Bovine respiratory disease complex (BRDC) is a leading cause of morbidity and mortality in pre-weaned calves, yet the role of commensal nasal microbiota in outbreak severity remains poorly understood. This study characterized nasal bacterial communities during two BRDC outbreaks of differing severity (moderate vs. severe) and at ~30 days post-treatment. Nasal swabs were collected from calves and analyzed using 16S rRNA gene sequencing (V1-V3 regions, Illumina MiSeq) and quantitative PCR targeting three major BRDC pathogens. Microbial community profiles differed between outbreak groups and across timepoints. Calves in the severe outbreak group exhibited lower microbial diversity compared to those in the moderate outbreak. In both groups, diversity significantly increased from outbreak to post-treatment. At the time of disease, nasal communities were dominated by the genera Mycoplasmopsis, Mesomycoplasma, and Caviibacter, with qPCR confirming Mycoplasma bovirhinis as the predominant species. These findings indicate that BRDC outbreaks in pre-weaned calves are associated with reduced microbial diversity and the dominance of pathogenic Mycoplasma species, with recovery characterized by greater bacterial diversity. Shifts in nasal microbiome composition between outbreak and post-treatment may reflect pathogen-driven disruption during disease and subsequent microbial community rebalancing.