Abstract
BackgroundThe importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract. Consequently, we have little understanding of the relationship between upper and lower respiratory tract microbiota in healthy cattle. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Nasopharyngeal swabs (NPS), and bronchoalveolar lavage (BAL) fluid, were collected from clinically healthy feedlot calves (n = 8). Genomic DNA from each sample was extracted, and the V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using Illumina Miseq platform.ResultsAcross all samples, the most predominant phyla were Proteobacteria, Actinobacteria and Firmicutes. The most common genera were Rathayibacter, Mycoplasma, Bibersteinia and Corynebacterium. The microbial community structure was distinct between these two biogeographical sites. Most of the bacterial genera identified in the BAL samples were also present in the NPS, but biogeographical-specific genera were enriched in both the NPS (Rathayibacter) and BAL (Bibersteinia) samples. There were strong associations between the presence of certain taxa at each specific location, and strong correlations between the presence of specific taxa in both the NPS and BAL samples.ConclusionsThe correlation between the presence of specific taxa in both the NPS and BAL samples, supports the notion of a mutualistic interrelationship between these microbial communities. Future studies, in large cohorts of animals, are needed to determine the role and clinical importance of the relationships of respiratory tract microbial communities with health, productivity, and susceptibility to the development of respiratory disease, in growing cattle.
Highlights
The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established
Technical advances in culture-independent techniques have shown that the respiratory tract of healthy people is not sterile, but is composed of a complex and previously unappreciated microbial community [16, 17], and that certain configurations of the microbiota may be associated with development of respiratory disease [18]
Overall sequence analysis The sequencing analysis of the V3-V4 hypervariable regions of the bacterial 16S Ribosomal ribo nucleic acid (rRNA) resulted in a total of 298,875 sequences in all Nasopharyngeal swabs (NPS) and bronchoalveolar lavage (BAL) samples
Summary
The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Characterization of the cattle microbiota has relied heavily on culture-dependent techniques which have mainly focused on the identification of major pathogens that can be cultured While useful, this approach is unable to provide information on those organisms that cannot be cultured, but are likely present at these sites, and so only provides a narrow understanding of the complexity of these clinically important microbial ecosystems [6]. In view of the importance of respiratory disease to the industry, our objectives were to characterize the composition and structure of the upper and lower respiratory microbiota, and to determine the relationship between the nasopharyngeal and bronchoalveolar microbiotas in clinically healthy feedlot cattle
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