Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattleReport as inadecuate




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BMC Microbiology

, 17:138

Ecological and evolutionary microbiology

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.

KeywordsFeedlot Microbiota,16S rRNA gene Next generation sequencing Respiratory tract AbbreviationsBALBroncho alveolar lavage

BRDBovine respiratory disease

DNADeoxyribonucleic acid

LDALinear discriminant analysis

LEfSeLinear discriminant analysis effective size

NPSNasopharyngeal swabs

OTUOperational taxonomic unit

PCoAPrinciple coordinate analysis

QIIMEQuantitative Insights Into Microbial Ecology

rRNARibosomal ribo nucleic acid

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

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Author: Mohamed M. Zeineldin - James F. Lowe - Elsbeth D. Grimmer - Maria R. C. de Godoy - Mohamed M. Ghanem - Yassein M. Ab

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