Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease

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 processing at the feedlot, and again at the initial diagnosis of BRD (n = 22). Clinically healthy pen matched controls calves (n = 10) were sampled at the same time as the BRD affected animals. Genomic DNA was extracted from each sample, and the 16S rRNA gene V1-V3 hypervariable region was amplified and sequenced using the Illumina MiSeq platform. Across all the samples, the predominant bacterial phyla were Proteobacteria, Firmicutes and Actinobacteria. While the predominant genera were Moraxella, Mycoplasma and Acinetobacter. Linear discriminant analysis (LDA) effect size (LEfSe) revealed significant differences in bacterial taxa between healthy and BRD affected calves. Discriminant analysis revealed that the nasopharyngeal microbiota in feedlot calves at entry and in BRD affected calves were distinct from pen matched healthy calves. While the temporal dynamics of this shift were not examined in this study, it is possible that the observed changes in mucosal microbiota are linked to the increased susceptibility of calves to BRD during the first month after entry in to the feedlot. Additional studies are needed to examine the trajectory of change in nasopharyngeal microbial communities from entry to disease onset, and to explore the impact of other factors such as diet transition, commingling, vaccination and housing on the nasopharyngeal microbiota of growing cattle.