Bovine respiratory disease (BRD) is one of the most serious causes of health and economic problems in the beef production industry, especially in recently weaned, intensely raised and newly transported feedlot cattle. While the importance of upper airway structure and function in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established, the role of the mucosal microbiota in respirtatory health is less well defined. The objective of this study was to characterize the nasopharyngeal microbiota of feedlot cattle at entry into a commercial feedlot, during initial management processing, and to compare the dynamics of change in these microbial communities between clinically healthy calves and those that develop BRD within the first month after entry. Deep nasopharyngeal swabs were collected from randomly selected healthy calves (n = 66) during initial handling and …