Comparative genomics and genome biology of Campylobacter showae
ABSTRACTCampylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2019-01-01
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| Series: | Emerging Microbes and Infections |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2019.1622455 |
| _version_ | 1797385766471467008 |
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| author | Tiffany Hsu Matthew R. Gemmell Eric A. Franzosa Susan Berry Indrani Mukhopadhya Richard Hansen Monia Michaud Hans Nielsen William G. Miller Henrik Nielsen Mona Bajaj-Elliott Curtis Huttenhower Wendy S. Garrett Georgina L. Hold |
| author_facet | Tiffany Hsu Matthew R. Gemmell Eric A. Franzosa Susan Berry Indrani Mukhopadhya Richard Hansen Monia Michaud Hans Nielsen William G. Miller Henrik Nielsen Mona Bajaj-Elliott Curtis Huttenhower Wendy S. Garrett Georgina L. Hold |
| author_sort | Tiffany Hsu |
| collection | DOAJ |
| description | ABSTRACTCampylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn’s disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential. |
| first_indexed | 2024-03-08T21:59:00Z |
| format | Article |
| id | doaj.art-72621a9f99264a12a5ca4b5b044904e0 |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-03-08T21:59:00Z |
| publishDate | 2019-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-72621a9f99264a12a5ca4b5b044904e02023-12-19T16:09:57ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512019-01-018182784010.1080/22221751.2019.1622455Comparative genomics and genome biology of Campylobacter showaeTiffany Hsu0Matthew R. Gemmell1Eric A. Franzosa2Susan Berry3Indrani Mukhopadhya4Richard Hansen5Monia Michaud6Hans Nielsen7William G. Miller8Henrik Nielsen9Mona Bajaj-Elliott10Curtis Huttenhower11Wendy S. Garrett12Georgina L. Hold13Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USASchool of Medicine, Medical Sciences and Nutrition, Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UKDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USASchool of Medicine, Medical Sciences and Nutrition, GI Research Group, University of Aberdeen, Aberdeen, UKSchool of Medicine, Medical Sciences and Nutrition, GI Research Group, University of Aberdeen, Aberdeen, UKDepartment of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, UKDepartments of Genetics and Complex Diseases and Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, USADepartment of Clinical Microbiology, Aalborg University Hospital, Aalborg, DenmarkProduce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Albany, USADepartment of Infectious Diseases, Aalborg University Hospital Aalborg, DenmarkInfection, Immunity, Inflammation Programme, UCL Great Ormond Street Institute of Child Health, London, UKDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USADepartments of Genetics and Complex Diseases and Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, USADepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USAABSTRACTCampylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn’s disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential.https://www.tandfonline.com/doi/10.1080/22221751.2019.1622455Campylobacter showaecomparative genomicsgenome biologygastrointestinal diseasebacterial virulence factorsbacterial secretion systems |
| spellingShingle | Tiffany Hsu Matthew R. Gemmell Eric A. Franzosa Susan Berry Indrani Mukhopadhya Richard Hansen Monia Michaud Hans Nielsen William G. Miller Henrik Nielsen Mona Bajaj-Elliott Curtis Huttenhower Wendy S. Garrett Georgina L. Hold Comparative genomics and genome biology of Campylobacter showae Emerging Microbes and Infections Campylobacter showae comparative genomics genome biology gastrointestinal disease bacterial virulence factors bacterial secretion systems |
| title | Comparative genomics and genome biology of Campylobacter showae |
| title_full | Comparative genomics and genome biology of Campylobacter showae |
| title_fullStr | Comparative genomics and genome biology of Campylobacter showae |
| title_full_unstemmed | Comparative genomics and genome biology of Campylobacter showae |
| title_short | Comparative genomics and genome biology of Campylobacter showae |
| title_sort | comparative genomics and genome biology of campylobacter showae |
| topic | Campylobacter showae comparative genomics genome biology gastrointestinal disease bacterial virulence factors bacterial secretion systems |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2019.1622455 |
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