Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism

William G Miller, Emma Yee, Bruno Lopes, Mary H. Chapman, Steven Huynh, James L. Bono, Craig T Parker, Norval J. C. Strachan, Ken J. Forbes

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The non-thermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g. cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but non-identical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins and the selenocysteinyl tRNA.
Original languageEnglish
Pages (from-to)1843-1858
Number of pages12
JournalGenome biology and evolution
Volume9
Issue number7
Early online date10 May 2017
DOIs
Publication statusPublished - 10 May 2017

Fingerprint

Campylobacter
Selenium
selenium
genomics
Fetus
genome
metabolism
Campylobacter lanienae
Genome
fetus
Campylobacter fetus
CRISPR-Cas Systems
gene
Campylobacter hyointestinalis
Selenoproteins
Selenocysteine
selenocysteine
Genes
selenoproteins
Flagellin

Keywords

  • campylobacter
  • C. lanienae
  • C. fetus
  • selenium
  • flagella

Cite this

Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism. / Miller, William G; Yee, Emma; Lopes, Bruno; Chapman, Mary H.; Huynh, Steven ; Bono, James L.; Parker, Craig T; Strachan, Norval J. C.; Forbes, Ken J.

In: Genome biology and evolution, Vol. 9, No. 7, 10.05.2017, p. 1843-1858.

Research output: Contribution to journalArticle

Miller, William G ; Yee, Emma ; Lopes, Bruno ; Chapman, Mary H. ; Huynh, Steven ; Bono, James L. ; Parker, Craig T ; Strachan, Norval J. C. ; Forbes, Ken J. / Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism. In: Genome biology and evolution. 2017 ; Vol. 9, No. 7. pp. 1843-1858.
@article{5af5ecdc1fc7441bb88ab6c5d7b9842e,
title = "Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism",
abstract = "The non-thermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g. cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but non-identical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins and the selenocysteinyl tRNA.",
keywords = "campylobacter, C. lanienae, C. fetus, selenium, flagella",
author = "Miller, {William G} and Emma Yee and Bruno Lopes and Chapman, {Mary H.} and Steven Huynh and Bono, {James L.} and Parker, {Craig T} and Strachan, {Norval J. C.} and Forbes, {Ken J.}",
note = "Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US. This work was funded by the United States Department of Agriculture, Agricultural Research Service, CRIS projects 2030-42000-230-047 and 2030-42000-230-051, and Food Standards Scotland project S14054",
year = "2017",
month = "5",
day = "10",
doi = "10.1093/gbe/evx093",
language = "English",
volume = "9",
pages = "1843--1858",
journal = "Genome biology and evolution",
issn = "1759-6653",
publisher = "Oxford University Press",
number = "7",

}

TY - JOUR

T1 - Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism

AU - Miller, William G

AU - Yee, Emma

AU - Lopes, Bruno

AU - Chapman, Mary H.

AU - Huynh, Steven

AU - Bono, James L.

AU - Parker, Craig T

AU - Strachan, Norval J. C.

AU - Forbes, Ken J.

N1 - Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US. This work was funded by the United States Department of Agriculture, Agricultural Research Service, CRIS projects 2030-42000-230-047 and 2030-42000-230-051, and Food Standards Scotland project S14054

PY - 2017/5/10

Y1 - 2017/5/10

N2 - The non-thermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g. cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but non-identical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins and the selenocysteinyl tRNA.

AB - The non-thermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g. cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but non-identical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins and the selenocysteinyl tRNA.

KW - campylobacter

KW - C. lanienae

KW - C. fetus

KW - selenium

KW - flagella

U2 - 10.1093/gbe/evx093

DO - 10.1093/gbe/evx093

M3 - Article

VL - 9

SP - 1843

EP - 1858

JO - Genome biology and evolution

JF - Genome biology and evolution

SN - 1759-6653

IS - 7

ER -