Abstract
BackgroundThe microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves.ResultsThe microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05).ConclusionsUsing 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.
Highlights
The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available
In one of the nine animals presenting clinical signs, the Deoxyribonucleic acid (DNA) concentration was below 5 ng/μl in both the nasal swab (NS) and trans-tracheal aspiration (TTA) samples; this animal was excluded from the study
Comparison by farm of origin showed a statistical difference in microbiota composition only for the NS samples. This suggests that the lower respiratory tract microbiota may be more homogeneous and resilient than the upper respiratory tract, in agreement with the results found in the dog [43]
Summary
The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. We used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. The 16S rRNA gene metabarcoding approach applied to lower respiratory tract samples from humans led to the discovery that the lung is not sterile even in healthy conditions [2]. Recent studies have shown that the microbiota of the lung could be considered an ecosystem and that its composition depends on the immigration, elimination, and reproduction rates of the microbial communities present there [4,5,6]. DNA metabarcoding analysis of pathological respiratory samples led to the hypothesis that alteration of the lung microbiota could assume a key role in the pathogenesis of human lung diseases, including bacterial pneumonia [6, 7]
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