Comparative genomics and genome biology of Campylobacter showae

Tiffany Hsu, Matthew R. Gemmell, Eric A. Franzosa, Susan H. 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 (Corresponding Author)

Research output: Contribution to journalArticle

Abstract

Campylobacter 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.
Original languageEnglish
Pages (from-to)827-840
Number of pages14
JournalEmerging Microbes and Infections
Volume8
Issue number1
Early online date6 Jun 2019
DOIs
Publication statusPublished - 2019

Fingerprint

Campylobacter
Genomics
Genome
Genes
CRISPR-Associated Proteins
Metagenome
Genome Size
Gingivitis
Periodontitis
Microbiota
Gastroenteritis
Inflammatory Bowel Diseases
Tongue
Adenoma
Virulence
Colorectal Neoplasms
Bacteria
Proteins

Keywords

  • Campylobacter showae
  • comparative genomics
  • genome biology
  • gastrointestinal disease
  • bacterial virulence factors
  • bacterial secretion systems
  • CELLS
  • BACTERIA
  • PROTEIN
  • CONCISUS
  • INVASION
  • JEJUNI
  • HELICOBACTER-PYLORI

Cite this

Hsu, T., Gemmell, M. R., Franzosa, E. A., Berry, S. H., Mukhopadhya, I., Hansen, R., ... Hold, G. L. (2019). Comparative genomics and genome biology of Campylobacter showae. Emerging Microbes and Infections, 8(1), 827-840. https://doi.org/10.1080/22221751.2019.1622455

Comparative genomics and genome biology of Campylobacter showae. / Hsu, Tiffany; Gemmell, Matthew R.; Franzosa, Eric A.; Berry, Susan H.; Mukhopadhya, Indrani; Hansen, Richard; Michaud, Monia; Nielsen, Hans; Miller, William G.; Nielsen, Henrik; Bajaj-Elliott, Mona; Huttenhower, Curtis; Garrett, Wendy S.; Hold, Georgina L. (Corresponding Author).

In: Emerging Microbes and Infections, Vol. 8, No. 1, 2019, p. 827-840.

Research output: Contribution to journalArticle

Hsu, T, Gemmell, MR, Franzosa, EA, Berry, SH, Mukhopadhya, I, Hansen, R, Michaud, M, Nielsen, H, Miller, WG, Nielsen, H, Bajaj-Elliott, M, Huttenhower, C, Garrett, WS & Hold, GL 2019, 'Comparative genomics and genome biology of Campylobacter showae' Emerging Microbes and Infections, vol. 8, no. 1, pp. 827-840. https://doi.org/10.1080/22221751.2019.1622455
Hsu, Tiffany ; Gemmell, Matthew R. ; Franzosa, Eric A. ; Berry, Susan H. ; Mukhopadhya, Indrani ; Hansen, Richard ; Michaud, Monia ; Nielsen, Hans ; Miller, William G. ; Nielsen, Henrik ; Bajaj-Elliott, Mona ; Huttenhower, Curtis ; Garrett, Wendy S. ; Hold, Georgina L. / Comparative genomics and genome biology of Campylobacter showae. In: Emerging Microbes and Infections. 2019 ; Vol. 8, No. 1. pp. 827-840.
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abstract = "Campylobacter 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.",
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AU - Hold, Georgina L.

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