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dc.contributor.authorJohnston, Dayle*
dc.contributor.authorEarley, Bernadette*
dc.contributor.authorCormican, Paul*
dc.contributor.authorMurray, Gerard*
dc.contributor.authorKenny, David A.*
dc.contributor.authorWaters, Sinead M.*
dc.contributor.authorMcGee, Mark*
dc.contributor.authorKelly, Alan K*
dc.contributor.authorMcCabe, Matthew*
dc.date.accessioned2017-08-16T16:27:54Z
dc.date.available2017-08-16T16:27:54Z
dc.date.issued2017-05-02
dc.identifier.citationJohnston D, Earley B, Cormican P, Murray G, Kenny DA, Waters SM, McGee M, Kelly AK, McCabe MS. Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. BMC Veterinary Research 2017;13; doi 118 10.1186/s12917-017-1035-2.en_GB
dc.identifier.urihttp://hdl.handle.net/11019/1495
dc.descriptionpeer-revieweden_GB
dc.description.abstractBackground Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.en_GB
dc.description.sponsorshipThis research, including all experimental procedures, was funded by the Irish Government under the National Development Plan 2007–2013, Department of Agriculture, Food and the Marine (DAFM) Research Stimulus Fund 11/S/131 (B. Earley, Principal Investigator) and EU project: 311,825 (B. Earley, Principal Investigator). The healthy calves were part of a study funded by DAFM Research Stimulus Fund 11/S/322 (D.A. Kenny, Principal Investigator).en_GB
dc.language.isoenen_GB
dc.publisherBiomed Centralen_GB
dc.relation.ispartofseriesBMC Veterinary Research;vol 13
dc.subjectBovine respiratory disease (BRD)en_GB
dc.subjectNGS 16S amplicon analysisen_GB
dc.subjectQuantitative insights into microbial ecology (QIIME)en_GB
dc.subjectDiagnosticsen_GB
dc.subjectlung microbiomeen_GB
dc.titleIllumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissueen_GB
dc.typeArticleen_GB
dc.date.updated2017-05-02T16:02:28Z
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dc.identifier.rmisGEAB-0204-6476
dc.identifier.doihttp://dx.doi.org/10.1186/s12917-017-1035-2
dc.contributor.sponsorDepartment of Agriculture, Food and the Marine
dc.contributor.sponsorEuropean Union
dc.contributor.sponsorGrantNumber11/S/131
dc.contributor.sponsorGrantNumber311,825
refterms.dateFOA2018-01-12T08:53:33Z


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