There is significant interest in understanding the respiratory microbiome; specifically, how certain phenotypes may relate to disease susceptibility in dairy calves. Potential relevance of these data includes improved screening diagnostics and development of respiratory probiotics. While many survey studies have been performed, this is the first study, to the authors' knowledge, to investigate short-term effects of an experimental bacterial challenge on the upper and lower respiratory tract microbiota. The purpose and primary objective of this study was to evaluate whether bacterial composition and diversity characteristics of the nasopharyngeal (NP) microbiota were protective against pneumonia following experimental challenge with Pasteurella multocida. The secondary objectives of this study were to evaluate the effects of bacterial challenge and ampicillin therapy on the NP, tonsillar, tracheobronchial lymph node and lung microbiota of pre-weaned dairy calves.
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