Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.

Liu, F; Chen, S; Luu, LDW; Lee, SA; Tay, ACY; Wu, R; Riordan, SM; Lan, R; Liu, L; Zhang, L

Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.

Liu, F Chen, S Luu, LDW Lee, SA Tay, ACY Wu, R Riordan, SM Lan, R Liu, L Zhang, L

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Publisher:: MICROBIOLOGY SOC
Publication Type:: Journal Article
Citation:: Microb Genom, 2020, 6, (11), pp. 1-13
Issue Date:: 2020-11

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Field	Value	Language
dc.contributor.author	Liu, F
dc.contributor.author	Chen, S
dc.contributor.author	Luu, LDW
dc.contributor.author	Lee, SA
dc.contributor.author	Tay, ACY
dc.contributor.author	Wu, R
dc.contributor.author	Riordan, SM
dc.contributor.author	Lan, R
dc.contributor.author	Liu, L
dc.contributor.author	Zhang, L
dc.date.accessioned	2022-10-31T06:20:42Z
dc.date.available	2022-10-31T06:20:42Z
dc.date.issued	2020-11
dc.identifier.citation	Microb Genom, 2020, 6, (11), pp. 1-13
dc.identifier.issn	2057-5858
dc.identifier.issn	2057-5858
dc.identifier.uri	http://hdl.handle.net/10453/163076
dc.description.abstract	Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 C. concisus strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete C. concisus genomes were analysed using bioinformatic tools. The enteric disease associations of C. concisus plasmids were examined using 239 C. concisus strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete C. concisus genomes in this study. Analysis of 16 complete C. concisus genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in C. concisus and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete C. concisus genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding C. concisus plasmids, genomospecies features, evolution, secretion systems and pathogenicity.
dc.format	Print
dc.language	eng
dc.publisher	MICROBIOLOGY SOC
dc.relation.ispartof	Microb Genom
dc.relation.isbasedon	10.1099/mgen.0.000457
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0604 Genetics, 0605 Microbiology
dc.subject.mesh	Base Composition
dc.subject.mesh	Campylobacter
dc.subject.mesh	Campylobacter Infections
dc.subject.mesh	Colitis, Ulcerative
dc.subject.mesh	Computational Biology
dc.subject.mesh	Genome, Bacterial
dc.subject.mesh	Humans
dc.subject.mesh	Phylogeny
dc.subject.mesh	Plasmids
dc.subject.mesh	Type VI Secretion Systems
dc.subject.mesh	Whole Genome Sequencing
dc.subject.mesh	Humans
dc.subject.mesh	Campylobacter
dc.subject.mesh	Campylobacter Infections
dc.subject.mesh	Colitis, Ulcerative
dc.subject.mesh	Computational Biology
dc.subject.mesh	Phylogeny
dc.subject.mesh	Base Composition
dc.subject.mesh	Genome, Bacterial
dc.subject.mesh	Plasmids
dc.subject.mesh	Type VI Secretion Systems
dc.subject.mesh	Whole Genome Sequencing
dc.title	Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.
dc.type	Journal Article
utslib.citation.volume	6
utslib.location.activity	England
utslib.for	0604 Genetics
utslib.for	0605 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/Faculty of Science/School of Life Sciences
utslib.copyright.status	open_access	*
dc.date.updated	2022-10-31T06:19:41Z
pubs.issue	11
pubs.publication-status	Published
pubs.volume	6
utslib.citation.issue	11

Abstract:

Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 C. concisus strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete C. concisus genomes were analysed using bioinformatic tools. The enteric disease associations of C. concisus plasmids were examined using 239 C. concisus strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete C. concisus genomes in this study. Analysis of 16 complete C. concisus genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in C. concisus and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete C. concisus genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding C. concisus plasmids, genomospecies features, evolution, secretion systems and pathogenicity.

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http://hdl.handle.net/10453/163076