The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media

Svetlana F Lima, Andre Gustavo V Teixeira, Catherine H Higgins, Fabio S Lima, Rodrigo C Bicalho, Svetlana F Lima, Andre Gustavo V Teixeira, Catherine H Higgins, Fabio S Lima, Rodrigo C Bicalho

Abstract

The upper respiratory tract (URT) hosts a complex microbial community of commensal microorganisms and potential pathogens. Analyzing the composition and nature of the healthy URT microbiota and how it changes over time will contribute to a better understanding of the pathogenesis of pneumonia and otitis. A longitudinal study was conducted including 174 Holstein calves that were divided in four groups: healthy calves, calves diagnosed with pneumonia, otitis or both diseases. Deep pharyngeal swabs were collected on days 3, 14, 28, and 35 of life, and next-generation sequencing of the 16S rRNA gene as well as quantitative PCR was performed. The URT of Holstein dairy calves aged 3 to 35 days revealed to host a highly diverse bacterial community. The relative abundances of the bacterial genera Mannheimia, Moraxella, and Mycoplasma were significantly higher in diseased versus healthy animals, and the total bacterial load of newborn calves at day 3 was higher for animals that developed pneumonia than for healthy animals. Our results corroborate the existing knowledge that species of Mannheimia and Mycoplasma are important pathogens in pneumonia and otitis. Furthermore, they suggest that species of Moraxella can potentially cause the same disorders (pneumonia and otitis), and that high neonatal bacterial load is a key contributor to the development of pneumonia.

Figures

Figure 1
Figure 1
Bar graphs illustrating the number of reads (A), Chao 1 richness index (B) and Shannon diversity index (C) for different postnatal ages. Error bars represent standard errors. Dunnett’s multiple comparison procedure was used to compare each disease status (otitis, pneumonia, and pneumonia-otitis combined) against the status “healthy” within each sample collection date.
Figure 2. Mean log10 number of the…
Figure 2. Mean log10 number of the 16S rRNA gene identified in upper respiratory tract samples of calves at various postnatal time points (3, 14, 28 and 35 days) and for different health statuses (healthy, pneumonia, and otitis).
Dunnett’s multiple comparison procedure was used to compare each disease status (otitis, pneumonia, and pneumonia-otitis combined) against the status “healthy” within each sample collection date. An asterisk between health statuses represents a significant difference (P < 0.05) for the age sampled.
Figure 3. Mean relative abundance of the…
Figure 3. Mean relative abundance of the most prevalent bacterial phyla identified in upper respiratory tract samples of calves at various postnatal time points (3, 14, 28 and 35 days) and for different health statuses (healthy, pneumonia, otitis, and pneumonia-otitis combined).
Figure 4
Figure 4
Mean relative abundance of the genus Mannheimia (A) and Mycoplasma (B) according to postnatal age at sample collection (3, 14, 28, 35 days) and health status (healthy, otitis, pneumonia, and pneumonia-otitis combined). Error bars are positioned around the means and represent the standard error of the mean. Dunnett’s multiple comparison procedure was used to compare each disease status (otitis, pneumonia, and pneumonia-otitis combined) against the status “healthy” within each sample collection time point. Asterisks on a series of data points indicate a significant difference (P 

Figure 5

Mean relative abundance of the…

Figure 5

Mean relative abundance of the genus Moraxella (A) and Pasteurella (B) according to…

Figure 5
Mean relative abundance of the genus Moraxella (A) and Pasteurella (B) according to postnatal age at sample collection (3, 14, 28, 35 days) and health status (healthy, otitis, pneumonia, and pneumonia-otitis combined). Error bars are positioned around the means and represent the standard error of the mean. Dunnett’s multiple comparison procedure was used to compare each disease status (otitis, pneumonia, and pneumonia-otitis combined) against the status “healthy” within each sample collection time point. Asterisks on a series of data points indicate a significant difference (P 
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Figure 5
Figure 5
Mean relative abundance of the genus Moraxella (A) and Pasteurella (B) according to postnatal age at sample collection (3, 14, 28, 35 days) and health status (healthy, otitis, pneumonia, and pneumonia-otitis combined). Error bars are positioned around the means and represent the standard error of the mean. Dunnett’s multiple comparison procedure was used to compare each disease status (otitis, pneumonia, and pneumonia-otitis combined) against the status “healthy” within each sample collection time point. Asterisks on a series of data points indicate a significant difference (P 

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