close
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 May;76(10):3071-81.
doi: 10.1128/AEM.02551-09. Epub 2010 Mar 26.

The internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genus

Si Ming Man  1 , Nadeem O Kaakoush, Sophie Octavia, Hazel Mitchell
Affiliations

The internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genus

Si Ming Man et al. Appl Environ Microbiol. 2010 May.

Abstract

The Campylobacter genus consists of a number of important human and animal pathogens. Although the 16S rRNA gene has been used extensively for detection and identification of Campylobacter species, there is currently limited information on the 23S rRNA gene and the internal transcribed spacer (ITS) region that lies between the 16S and 23S rRNA genes. We examined the potential of the 23S rRNA gene and the ITS region to be used in species differentiation and delineation of systematic relationships for 30 taxa within the Campylobacter genus. The ITS region produced the highest mean pairwise percentage difference (35.94%) compared to the 16S (5.34%) and 23S (7.29%) rRNA genes. The discriminatory power for each region was further validated using Simpson's index of diversity (D value). The D values were 0.968, 0.995, and 0.766 for the ITS region and the 23S and 16S rRNA genes, respectively. A closer examination of the ITS region revealed that Campylobacter concisus, Campylobacter showae, and Campylobacter fetus subsp. fetus harbored tRNA configurations not previously reported for other members of the Campylobacter genus. We also observed the presence of strain-dependent intervening sequences in the 23S rRNA genes. Neighbor-joining trees using the ITS region revealed that Campylobacter jejuni and Campylobacter coli strains clustered in subgroups, which was not observed in trees derived from the 16S or 23S rRNA gene. Of the three regions examined, the ITS region is by far the most cost-effective region for the differentiation and delineation of systematic relationships within the Campylobacter genus.

PubMed Disclaimer

Figures

FIG. 1.
FIG. 1.
Schematic representation of the 18 forward (→) and reverse (←) primers and their target positions within the 16S-ITS-23S rRNA operon.
FIG. 2.
FIG. 2.
Neighbor-joining (NJ) trees based on Campylobacter sequences derived from the 16S rRNA gene (A), 23S rRNA gene (B), ITS region (C), and all three regions combined (D). Each taxon is labeled by species and strain number, and in brackets is the original source of isolation. Bootstrap values, if greater than 50%, are presented at nodes of the tree.
FIG. 2.
FIG. 2.
Neighbor-joining (NJ) trees based on Campylobacter sequences derived from the 16S rRNA gene (A), 23S rRNA gene (B), ITS region (C), and all three regions combined (D). Each taxon is labeled by species and strain number, and in brackets is the original source of isolation. Bootstrap values, if greater than 50%, are presented at nodes of the tree.
FIG. 3.
FIG. 3.
The representative secondary structures of the Campylobacter 23S rRNA molecule using C. curvus 525.92. Shown is the 23S rRNA secondary structure with (A) and without (B) the 240-bp IVS. The spatial distribution of IVS within the secondary structure of the 23S rRNA is indicated in a box (A). The predicted secondary structures of two resultant fragmented 23S rRNA molecules are shown in panels C and D. The locations of the neighboring regions are represented by triangles.
See this image and copyright information in PMC

References

    1. Alderton, M. R., V. Korolik, P. J. Coloe, F. E. Dewhirst, and B. J. Paster. 1995. Campylobacter hyoilei sp. nov., associated with porcine proliferative enteritis. Int. J. Syst. Bacteriol. 45:61-66. - PubMed
    1. Allos, B. M. 2001. Campylobacter jejuni infections: update on emerging issues and trends. Clin. Infect. Dis. 32:1201-1206. - PubMed
    1. Al-Mashat, R. R., and D. J. Taylor. 1983. Production of enteritis in calves by the oral inoculation of pure cultures of Campylobacter fetus subspecies intestinalis. Vet. Rec. 112:54-58. - PubMed
    1. Boyer, S. L., V. R. Flechtner, and J. R. Johansen. 2001. Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in Cyanobacteria. Mol. Biol. Evol. 18:1057-1069. - PubMed
    1. Brodskiǐ, L. I., V. V. Ivanov, L. Kalaidzidis Ia, A. M. Leontovich, V. K. Nikolaev, S. I. Feranchuk, and V. A. Drachev. 1995. GeneBee-NET: an Internet based server for biopolymer structure analysis. Biokhimiia 60:1221-1230. - PubMed

LinkOut - more resources