Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.

Brito, BP; Frost, MJ; Anantanawat, K; Jaya, F; Batterham, T; Djordjevic, SP; Chang, W-S; Holmes, EC; Darling, AE; Kirkland, PD

Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.

Brito, BP Frost, MJ Anantanawat, K

Jaya, F Batterham, T Djordjevic, SP Chang, W-S Holmes, EC Darling, AE Kirkland, PD

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Publisher:: Springer Nature
Publication Type:: Journal Article
Citation:: Microbiome, 2023, 11, (1), pp. 158
Issue Date:: 2023-07-25

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Field	Value	Language
dc.contributor.author	Brito, BP
dc.contributor.author	Frost, MJ
dc.contributor.author	Anantanawat, K https://orcid.org/0000-0002-7862-0969
dc.contributor.author	Jaya, F
dc.contributor.author	Batterham, T
dc.contributor.author	Djordjevic, SP
dc.contributor.author	Chang, W-S
dc.contributor.author	Holmes, EC
dc.contributor.author	Darling, AE
dc.contributor.author	Kirkland, PD
dc.date.accessioned	2023-09-29T04:42:21Z
dc.date.available	2023-06-03
dc.date.available	2023-09-29T04:42:21Z
dc.date.issued	2023-07-25
dc.identifier.citation	Microbiome, 2023, 11, (1), pp. 158
dc.identifier.issn	2049-2618
dc.identifier.issn	2049-2618
dc.identifier.uri	http://hdl.handle.net/10453/172382
dc.description.abstract	BACKGROUND: Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. RESULTS: A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. CONCLUSION: This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.
dc.format	Electronic
dc.language	eng
dc.publisher	Springer Nature
dc.relation.ispartof	Microbiome
dc.relation.isbasedon	10.1186/s40168-023-01591-1
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0602 Ecology, 0605 Microbiology, 1108 Medical Microbiology
dc.subject.classification	3104 Evolutionary biology
dc.subject.classification	3107 Microbiology
dc.subject.mesh	Animals
dc.subject.mesh	Cattle
dc.subject.mesh	Rhinitis
dc.subject.mesh	Australia
dc.subject.mesh	Respiratory Tract Diseases
dc.subject.mesh	Viruses
dc.subject.mesh	Cattle Diseases
dc.subject.mesh	Animals
dc.subject.mesh	Cattle
dc.subject.mesh	Viruses
dc.subject.mesh	Respiratory Tract Diseases
dc.subject.mesh	Rhinitis
dc.subject.mesh	Cattle Diseases
dc.subject.mesh	Australia
dc.title	Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.
dc.type	Journal Article
utslib.citation.volume	11
utslib.location.activity	England
utslib.for	0602 Ecology
utslib.for	0605 Microbiology
utslib.for	1108 Medical Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - AIMI - Australian Institute for Microbiology & Infection
utslib.copyright.status	open_access	*
dc.date.updated	2023-09-29T04:42:15Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	11
utslib.citation.issue	1

Abstract:

BACKGROUND: Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. RESULTS: A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. CONCLUSION: This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.

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http://hdl.handle.net/10453/172382