Type

Journal Article

Authors

Matthew Sean McCabe
Alan Kieran Kelly
Mark McGee
Sinead Mary Waters
David Anthony Kenny
Gerard Murray
Paul Cormican
Bernadette Earley
Dayle Johnston

Subjects

Microbiology

Topics
respiratory disease bacteria analysis lung disease bovine tissue tissue analysis dna bacterial sequence analysis next generation sequencing

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. (2016)

Abstract 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. 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. 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.
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Full list of authors on original publication

Matthew Sean McCabe, Alan Kieran Kelly, Mark McGee, Sinead Mary Waters, David Anthony Kenny, Gerard Murray, Paul Cormican, Bernadette Earley, Dayle Johnston

Experts in our system

1
Matthew S. McCabe
Teagasc
Total Publications: 45
 
2
Alan K Kelly
Teagasc
Total Publications: 88
 
3
Mark McGee
Teagasc
Total Publications: 81
 
4
Sinead M. Waters
Teagasc
Total Publications: 99
 
5
D.A. Kenny
Teagasc
Total Publications: 147
 
6
Gerard M. Murray
Teagasc
Total Publications: 12
 
7
Paul Cormican
Teagasc
Total Publications: 54
 
8
Bernadette Earley
Teagasc
Total Publications: 120
 
9
Dayle Johnston
Teagasc
Total Publications: 10