Complete Genome Sequence of Campylobacter iguaniorum Strain RM11343, Isolated from an Alpaca

Miller, William G.; Yee, Emma; Huynh, Stephen; Chapman, Mary H.; Parker, Craig T.

doi:10.1128/genomea.00646-16

Cited by 6 publications

(6 citation statements)

References 14 publications

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“…To clarify the taxonomic structure of the C. fetus group and further characterize these putative novel taxa, the genomes of five strains, including the C. lanienae type strain NCTC 13004 and representatives of all three putative novel taxa, were sequenced to completion; additional genomes were sequenced to draft level. The genomes of all other described taxa within the C. fetus group have been sequenced to completion ( Gilbert et al 2013 , 2014 ; Miller et al 2016a , 2016b ; Oliveira et al 2016 ; Stynen et al 2011 ; van der Graaf-van Bloois et al 2014a , 2014b ); thus, a full comparative genomic analysis of the C. fetus group could be accomplished with the new genomic data.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Miller

Yee

Lopes

et al. 2017

Genome Biology and Evolution

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The nonthermotolerant 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 nonidentical, 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.

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Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Miller

Yee

Lopes

et al. 2017

Genome Biology and Evolution

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“…hyointestinalis DSM 19053 1 CR67_01870 Porcine intestine SAMN01176354 @ C. hyointestinalis ssp. lawsonii CCUG 27631 1 CHL_RS06765 Porcine intestine [ 37 ] C. iguaniorum RM11343 1 CIG11343_RS03950 Alpaca faeces [ 21 ] a Genome online database project ID. @ NCBI Biosample ID …”

Section: Resultsmentioning

confidence: 99%

“…In addition to C. concisus , a number of other Campylobacter species were recently reported to have the zot genes [ 17 – 21 ]. In this study, we found that Campylobacter zot genes formed two clusters (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to C. concisus , four additional Campylobacter species including Campylobacter ureolyticus , Campylobacter corcagiensis , Campylobacter gracilis and Campylobacter iguaniorum were recently reported to possess the zot gene [ 17 – 21 ]. The similarities of Zot proteins in different Campylobacter species have not been examined.…”

Section: Introductionmentioning

confidence: 99%

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Zonula occludens toxins and their prophages in Campylobacter species

et al. 2016

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BackgroundWe previously showed that zonula occludens toxin (Zot) encoded by Campylobacter concisus zot808T gene has the potential to initiate inflammatory bowel disease. This Zot protein caused prolonged intestinal epithelial barrier damage, induced intestinal epithelial and macrophage production of tumor necrosis factor-α and enhanced the responses of macrophages to other microbes. In order to understand the potential virulence of Zot proteins in other Campylobacter species, in this study we examined their presence, similarities, motifs and prophages.MethodsThe presence of Zot proteins in Campylobacter species was examined by searching for the Zot family domain in multiple protein databases. Walker A and Walker B motifs in Zot proteins were identified using protein sequence alignment. A phylogenetic tree based on Campylobacter zot genes was constructed using maximum-likelihood method. Campylobacter Zot proteins were compared using protein sequence alignment. The zot-containing prophages in Campylobacter species were identified and compared with known prophage proteins and other viral proteins using protein sequence alignment and protein BLAST.ResultsTwelve Zot proteins were found in nine Campylobacter species/subspecies. Among these Campylobacter species, three species had two Zot proteins and the remaining six species/subspecies had one Zot protein. Walker A and Walker B motifs and a transmembrane domain were found in all identified Campylobacter Zot proteins. The twelve Campylobacter zot genes from the nine Campylobacter species/subspecies formed two clusters. The ZotCampyType_1 proteins encoded by Cluster 1 Campylobacter zot genes showed high similarities to each other. However, ZotCampyType_2 proteins encoded by Cluster 2 Campylobacter zot genes were more diverse. Furthermore, the zot-containing Campylobacter prophages were identified.ConclusionThis study reports the identification of two types of Campylobacter Zot proteins. The high similarities of ZotCampyType_1 proteins suggest that they are likely to have similar virulence. ZotCampyType_2 proteins are less similar to each other and their virulent properties, if any, remain to be examined individually.Electronic supplementary materialThe online version of this article (doi:10.1186/s13099-016-0125-1) contains supplementary material, which is available to authorized users.

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“…Reported overall prevalence in reptiles based on culturing was 8.2%; 15.6% of the chelonians and 6.1% of the lizards, but none of the snakes examined, carried this Campylobacter species ( Gilbert et al 2014a ). Recently, Cig has also been isolated from a non-reptilian host ( Miller et al 2016a ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics ofCampylobacter iguaniorumto Unravel Genetic Regions Associated with Reptilian Hosts

et al. 2016

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Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, and C. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorum strain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated from a green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-associated C. fetus subsp. testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regions were identified in C. iguaniorum. One of these regions is > 50 kb with deviant G + C content, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-associated C. fetus subsp. testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

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Complete Genome Sequence of Campylobacter iguaniorum Strain RM11343, Isolated from an Alpaca

Abstract: Campylobacter iguaniorum is a member of the C. fetus group of campylobacters and is one of two Campylobacter taxa isolated from reptiles. This study describes the whole-genome sequence of the C. iguaniorum strain RM11343, which was isolated from a California alpaca fecal sample.

Cited by 6 publications

References 14 publications

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Zonula occludens toxins and their prophages in Campylobacter species

Comparative Genomics ofCampylobacter iguaniorumto Unravel Genetic Regions Associated with Reptilian Hosts

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