Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival

The composition of the nasopharyngeal bacterial microbiota has been shown to play a role in cattle respiratory health. However, previous studies are narrow in scope regarding longitudinal observations, limiting our understanding of how respiratory bacteria evolve over time. The objective was therefore to characterize this microbiota and its evolution over time in beef calves. A total of 120 crossbred beef-breed steer calves were enrolled in a study in southern Alberta at the time of first vaccination (spring processing), comprising three groups (40 calves/group) that originated from different ranches and were placed in different feedlots. Deep nasopharyngeal swab samples were collected from the calves at the time of spring processing, arrival at the feedlot, and a targeted 40 days after feedlot arrival. The swabs were processed for DNA extraction and the V4 region of the 16S rRNA gene was sequenced to evaluate the microbiota. The composition of the microbiota differed among groups of calves, with each group showing different relative abundances of 963 observed sequence variants. Mycoplasma was the most abundant genus and M. dispar the most abundant species across all groups. There was a distinct shift in the composition of the microbiota over time for all calf groups; however, changes in sequence variants differed by group. Variations in both microbiota composition and temporal changes of sequence variants according to calf group indicates that the respiratory microbiota of beef cattle may lack a common pattern of evolution from ranch to feedlot, and that future studies should account for potential group effects.