Comparison of the nasopharyngeal bacterial microbiota of beef calves raised without the use of antimicrobials between healthy calves and those diagnosed with bovine respiratory disease.

The role of the respiratory bacterial microbiota in the pathogenesis of bovine respiratory disease (BRD) is still not well defined, limiting our understanding of the disease. Specifically, there is no information on the nasopharyngeal bacterial microbiota of cattle raised without antimicrobials. The objective was to characterize and compare the nasopharyngeal bacterial microbiota in feedlot cattle raised without antimicrobials that were healthy or diagnosed with BRD. Newly-received feedlot cattle (arrival bodyweight ± SD = 218 ± 37 kg) with BRD (n = 82) and pen-matched controls (n = 82) were clinically examined and sampled by deep nasopharyngeal swab (DNS). DNA was extracted from each DNS and the 16S rRNA gene (V4) was sequenced. Alpha and beta diversity were compared between health groups and among 3 days-on-feed (DOF) groups (group A = 3-12 DOF; group B = 13-20 DOF; group C = 21-44 DOF). Observed species richness was lower (P = 0.031) in cattle with BRD compared to healthy ones. Both health status (P = 0.007) and DOF groups (P < 0.001) were sources of variation in microbiota composition. Differences between health groups were driven by multiple sequence variants, including Mycoplasma bovis, Histophilus somni, and several Moraxella spp. Notably, M. bovis was more frequently identified in cattle with BRD. M. bovis identification was also higher in cattle sampled at later DOF. The increased identification of M. bovis in cattle with BRD reaffirms a potentially significant role for this bacterium in respiratory health.