Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-1042-2) contains supplementary material, which is available to authorized users.

Microbiome of the upper nasal cavity of beef calves prior to weaning12

“…Furthermore, this predominance of the Promicromonospora genus was present in the upper nasal cavity of calves located at all 3 locations at USMARC and across the 2 yr evaluated, indicating that Promicromonospora is a common bacterial genus of the commensal microbiome at this sampling time point and age of calf. This bacterial genus has been reported previously (Zeineldin et al, 2017) as a pathogen present in nasal samples collected from cattle after weaning in the feedlot. 2018findings to the data herein shows a similar high abundance of the phylum Actinobacteria (Supplemental Figures 1A and 2A).…”

Topography of the respiratory tract bacterial microbiota in cattle

“…The characterization of distinct niche microbiota throughout the bovine respiratory tract is a novel finding. Compositional differences between URT and lower respiratory tract (LRT) microbiotas have been previously observed in cattle [13][14][15]. However, these past studies have been limited in scope, comparing only transtracheal aspirations or bronchoalveolar lavages to the nasopharynx.…”

The effects of saline water consumption on the ultrasonographic and histopathological appearance of the kidney and liver in Barki sheep

“…Statistical analyses were performed using JMP 13 software (SAS Institute Inc., Cary, NC, U.S.A.) [ 26 , 27 ]. The data were compared using a one-way analysis of variance (ANOVA) and pooled t -tests fitted in JMP 13 (SAS Institute Inc.).…”