The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung consolidation

Abstract

Preweaning is a high-risk time period for dairy calves; pneumonia is a predominant cause of mortality and use of antibiotics on farms. Given the concern of antibiotic resistance, there is demand to investigate alternative therapies. Administering probiotics to alter the respiratory microbiome and reduce the risk of pneumonia has shown promising results in mice. Although the bacterial community dynamics of the upper airway have been investigated in dairy calves, they have not been evaluated in calves diagnosed with pneumonia using lung ultrasound (US). By allowing visualization of lung consolidation, US increases the sensitivity of pneumonia diagnosis. Elucidating phenotypes of the commensal community in healthy and pneumonic dairy calves is crucial to investigating probiotics as a preventative for pneumonia. The primary objective of this prospective case-control study was to describe bacterial communities in the nasopharynx (NP) of preweaned dairy calves with and without lung consolidation. Secondary objectives included evaluating the effects of previous antibiotic therapy and age on the composition of NP microbiota.