An analysis of the universal target (UT) sequence from the gene was performed in order to evaluate its usefulness in phylogenetic and taxonomic studies and as an identification marker for the genus . Sequences of 555 bp, corresponding to the UT region, were obtained from a collection of 35 strains representing all of the species and subspecies of . From the analysis of these sequences, a range of divergence of 0–23.3 % was obtained, with a mean of 11.2±0.9 %. Comparative analyses between and , and 16S rRNA gene sequences were carried out from the same strain collection. Sequences of the UT region showed similar discriminatory power to and sequences. The phylogenetic relationships inferred from sequence distances indicated an excellent correlation with the present affiliation of species with the exception of subsp. , which appeared in a separate phylogenetic line, and , which exhibited a very loose phylogenetic relationship to the genus . Sequencing of from 33 additional strains also allowed us to establish intra- and interspecific threshold values. Intraspecific divergence rates were ≤3.5 %, while interspecific divergence rates fell between 3.7 and 16.9 %, excluding . In this study, UT sequencing was shown to be a universal, useful, simple and rapid method for the identification and phylogenetic affiliation of strains.

Keyword(s): UT, universal target

Article metrics loading...

Loading full text...

Full text loading...



  1. Abbott, S. L., Cheung, W. K. W. & Janda, J. M.(2003). The genus Aeromonas: biochemical characteristics, atypical reactions, and phenotypic identification schemes. J Clin Microbiol 41, 2348–2357.[CrossRef] [Google Scholar]
  2. Brousseau, R., Hill, J. E., Préfontaine, G., Goh, S. H., Harel, J. & Hemmingsen, S. M.(2001).Streptococcus suis serotypes characterized by analysis of chaperonin 60 gene sequences. Appl Environ Microbiol 67, 4828–4833.[CrossRef] [Google Scholar]
  3. Collins, M. D., Martínez-Murcia, A. J. & Cai, J.(1993).Aeromonas enteropelogenes and Aeromonas ichthiosmia are identical to Aeromonas trota and Aeromonas veronii, respectively, as revealed by small-subunit rRNA sequence analysis. Int J Syst Bacteriol 43, 855–856.[CrossRef] [Google Scholar]
  4. Esteve, C., Valera, L., Gutiérrez, C. & Ventosa, A.(2003). Taxonomic study of sucrose-positive Aeromonasjandaei-like isolates from faeces, water and eels: emendation of A. jandaei Carnahan et al. 1992. Int J Syst Evol Microbiol 53, 1411–1419.[CrossRef] [Google Scholar]
  5. Fares, M. A. & Travers, S. A.(2006). A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. Genetics 173, 9–23.[CrossRef] [Google Scholar]
  6. Goyal, K., Qamra, R. & Mande, S. C.(2006). Multiple gene duplication and rapid evolution in the groEL gene: functional implications. J Mol Evol 63, 781–787.[CrossRef] [Google Scholar]
  7. Gupta, R. S. & Sneath, P. H.(2007). Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions. J Mol Evol 64, 90–100.[CrossRef] [Google Scholar]
  8. Hickman-Brenner, F. W., Fanning, G. R., Arduino, M. J., Brenner, D. J. & Farmer, J. J., III(1988).Aeromonas schubertii, a new mannitol-negative species found in human clinical specimens. J Clin Microbiol 26, 1561–1564. [Google Scholar]
  9. Hill, J. E., Seipp, R. P., Betts, M., Hawkins, L., Van Kessel, A. G., Crosby, W. L. & Hemmingsen, S. M.(2002). Extensive profiling of a complex microbial community by high-throughput sequencing. Appl Environ Microbiol 68, 3055–3066.[CrossRef] [Google Scholar]
  10. Hill, J. E., Penny, S. L., Crowell, K. G., Goh, S. H. & Hemmingsen, S. M.(2004). cpnDB: a chaperonin sequence database. Genome Res 14, 1669–1675.[CrossRef] [Google Scholar]
  11. Hill, J. E., Paccagnella, A., Law, K., Melito, P. L., Woodward, D. L., Price, L., Leung, A. H., Ng, L. K., Hemmingsen, S. M. & Goh, S. H.(2006). Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55, 393–399.[CrossRef] [Google Scholar]
  12. Horwich, A. L., Fenton, W. A., Chapman, E. & Farr, G. W.(2007). Two families of chaperonin: physiology and mechanism. Annu Rev Cell Dev Biol 23, 115–145.[CrossRef] [Google Scholar]
  13. Huys, G. & Swings, J.(1999). Evaluation of a fluorescent amplified fragment length polymorphism (FAFLP) methodology for the genotypic discrimination of Aeromonas taxa. FEMS Microbiol Lett 177, 83–92.[CrossRef] [Google Scholar]
  14. Huys, G., Coopman, R., Janssen, P. & Kersters, K.(1996). High-resolution genotypic analysis of the genus Aeromonas by AFLP fingerprinting. Int J Syst Bacteriol 46, 572–580.[CrossRef] [Google Scholar]
  15. Huys, G., Kämpfer, P., Altwegg, M., Coopman, R., Janssen, P., Gillis, M. & Kersters, K.(1997). Inclusion of Aeromonas DNA hybridization group 11 in Aeromonas encheleia and extended descriptions of the species Aeromonas eucrenophila and A. encheleia. Int J Syst Bacteriol 47, 1157–1164.[CrossRef] [Google Scholar]
  16. Huys, G., Kämpfer, P. & Swings, J.(2001). New DNA-DNA hybridization and phenotypic data on the species Aeromonasichthiosmia and Aeromonasallosaccharophila: A. ichthiosmia Schubert et al. 1990 is a later synonym of A. veronii Hickman-Brenner et al. 1987. Syst Appl Microbiol 24, 177–182.[CrossRef] [Google Scholar]
  17. Huys, G., Denys, R. & Swings, J.(2002). DNA–DNA reassociation and phenotypic data indicate synonymy between Aeromonasenteropelogenes Schubert et al. 1990 and Aeromonastrota Carnahan et al. 1991. Int J Syst Evol Microbiol 52, 1969–1972.[CrossRef] [Google Scholar]
  18. Huys, G., Cnockaert, M. & Swings, J.(2005).Aeromonasculicicola Pidiyar et al. 2002 is a later subjective synonym of Aeromonasveronii Hickman-Brenner et al. 1987. Syst Appl Microbiol 28, 604–609.[CrossRef] [Google Scholar]
  19. Ihaka, R. & Gentleman, R.(1996). R: a language for data analysis and graphics. J Comput Graph Stat 5, 299–314. [Google Scholar]
  20. Jukes, T. H. & Cantor, C. R.(1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  21. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  22. Küpfer, M., Kuhnert, P., Korczak, B. M., Peduzzi, R. & Demarta, A.(2006). Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences. Int J Syst Evol Microbiol 56, 2743–2751.[CrossRef] [Google Scholar]
  23. Martin-Carnahan, A. & Joseph, S. W.(2005). Genus I. Aeromonas Stanier 1943, 213AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part B, pp. 557–578. Edited by G. M. Garrity, D. J. Brenner, N. R. Krieg & J. T. Staley. New York: Springer.
  24. Martínez-Murcia, A. J.(1999). Phylogenetic positions of Aeromonas encheleia, Aeromonas popoffii, Aeromonas DNA hybridization group 11 and Aeromonas group 501. Int J Syst Bacteriol 49, 1403–1408.[CrossRef] [Google Scholar]
  25. Martínez-Murcia, A. J., Soler, L., Saavedra, M. J., Chacón, M. R., Guarro, J., Stackebrandt, E. & Figueras, M. J.(2005). Phenotypic, genotypic, and phylogenetic discrepancies to differentiate Aeromonas salmonicida from Aeromonas bestiarum. Int Microbiol 8, 259–269. [Google Scholar]
  26. Martínez-Murcia, A. J., Figueras, M. J., Saavedra, M. J. & Stackebrandt, E.(2007). The recently proposed species Aeromonas sharmana sp. nov., isolate GPTSA-6T, is not a member of the genus Aeromonas. Int Microbiol 10, 61–64. [Google Scholar]
  27. Miñana-Galbis, D., Farfán, M., Lorén, J. G. & Fusté, M. C.(2002). Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain. J Appl Microbiol 93, 420–430.[CrossRef] [Google Scholar]
  28. Miñana-Galbis, D., Farfán, M., Fusté, M. C. & Lorén, J. G.(2004a).Aeromonas molluscorum sp. nov., isolated from bivalve molluscs. Int J Syst Evol Microbiol 54, 2073–2078.[CrossRef] [Google Scholar]
  29. Miñana-Galbis, D., Farfán, M., Fusté, M. C. & Lorén, J. G.(2004b). Genetic diversity and population structure of Aeromonas hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii by multilocus enzyme electrophoresis (MLEE). Environ Microbiol 6, 198–208.[CrossRef] [Google Scholar]
  30. Miñana-Galbis, D., Farfán, M., Fusté, M. C. & Lorén, J. G.(2007).Aeromonas bivalvium sp. nov., isolated from bivalve molluscs. Int J Syst Evol Microbiol 57, 582–587.[CrossRef] [Google Scholar]
  31. Nei, M.(1996). Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet 30, 371–403.[CrossRef] [Google Scholar]
  32. Nhung, P. H., Hata, H., Ohkusu, K., Noda, M., Shah, M. M., Goto, K. & Ezaki, T.(2007). Use of the novel phylogenetic marker dnaJ and DNA–DNA hybridization to clarify interrelationships within the genus Aeromonas. Int J Syst Evol Microbiol 57, 1232–1237.[CrossRef] [Google Scholar]
  33. Rozas, J. & Rozas, R.(1999). DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174–175.[CrossRef] [Google Scholar]
  34. Saavedra, M. J., Figueras, M. J. & Martínez-Murcia, A. J.(2006). Updated phylogeny of the genus Aeromonas. Int J Syst Evol Microbiol 56, 2481–2487.[CrossRef] [Google Scholar]
  35. Soler, L., Yáñez, M. A., Chacon, M. R., Aguilera-Arreola, M. G., Catalán, V., Figueras, M. J. & Martínez-Murcia, A. J.(2004). Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes. Int J Syst Evol Microbiol 54, 1511–1519.[CrossRef] [Google Scholar]
  36. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef] [Google Scholar]
  37. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  38. Thompson, J. R., Pacocha, S., Pharino, C., Klepac-Ceraj, V., Hunt, D. E., Benoit, J., Sarma-Rupavtarm, R., Distel, D. L. & Polz, M. F.(2005). Genotypic diversity within a natural coastal bacterioplankton population. Science 307, 1311–1313.[CrossRef] [Google Scholar]
  39. Valera, L. & Esteve, C.(2002). Phenotypic study by numerical taxonomy of strains belonging to the genus Aeromonas. J Appl Microbiol 93, 77–95.[CrossRef] [Google Scholar]
  40. Wick, G., Knoflach, M. & Xu, Q.(2004). Autoimmune and inflammatory mechanisms in atherosclerosis. Annu Rev Immunol 22, 361–403.[CrossRef] [Google Scholar]

Data & Media loading...


vol. , part 8, pp. 1976 - 1983

Scatter plots of pairwise JC69 distances.

Consensus neighbour-joining phylogenetic tree (JC69 distance) obtained from 71 UT sequences, encompassing all of the species and subspecies of the genus .

[PDF file of Supplementary Figs S1 and S2](115 KB)

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error