Comparative genomics and genome biology of Campylobacter showae

TY - JOUR

T1 - Comparative genomics and genome biology of Campylobacter showae

AU - Hsu, Tiffany

AU - Gemmell, Matthew R.

AU - Franzosa, Eric A.

AU - Berry, Susan

AU - Mukhopadhya, Indrani

AU - Hansen, Richard

AU - Michaud, Monia

AU - Nielsen, Hans

AU - Miller, William G.

AU - Nielsen, Henrik

AU - Bajaj-Elliott, Mona

AU - Huttenhower, Curtis

AU - Garrett, Wendy S.

AU - Hold, Georgina L.

N1 - Funding Information: This work was supported by NHS Grampian Endowments [grant number 2014/08]; US-UK Fulbright Commission to GH; NHS Research Scotland Career Researcher Fellowship to RH; National Institutes of Health NIDDK [grant number R24DK110499 to CH]; Chief Scientist Office Clinical Academic Fellowship [grant number CAF/08/01 to RH]; National Science Foundation [grant number DBI-1053486 to CH]. Publisher Copyright: © 2019 The Author(s).

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Bacterial secretion systems

KW - Bacterial virulence factors

KW - Campylobacter showae

KW - Comparative genomics

KW - Gastrointestinal disease

KW - Genome biology

UR - https://www.scopus.com/pages/publications/85067426611

U2 - 10.1080/22221751.2019.1622455

DO - 10.1080/22221751.2019.1622455

M3 - Article

C2 - 31169073

SN - 2222-1751

VL - 8

SP - 827

EP - 840

JO - Emerging Microbes and Infections

JF - Emerging Microbes and Infections

IS - 1

ER -