Journal List > Korean J Clin Microbiol > v.15(3) > 1038274

Kim and Jang: Basic Concepts of Bacterial Taxonomy

Abstract

The three components of taxonomy are classification, nomenclature and identification. Traditionally, bacterial classification and identification were performed based on the morphology and the biochemical data of the bacteria. In newer theories, or so-called natural concepts, the relationships between bacteria are based on the overall similarities of both the phenotypic and genotypic characteristics. The polyphasic taxonomy, or current taxonomy, describes the integration of all of the available genotypic, phenotypic, and phylogenetic information into a consensus type of general-purpose classification. When routine identification methods that are based on the biochemical tests fail, alternative procedures such as complete 16s rRNA gene sequence analysis are required. Although the results of 16s rRNA gene sequence analysis have not been fully discriminatory to differentiate closely related species, they may guide the additional analyses that are required for species identification.

Figures and Tables

Fig. 1
Schematic diagram showing procedure of multilocus sequence analysis (MLSA). The concatenated sequences of seven house keeping genes (HKG) are used for phylogentic analysis of four species of bacteria to improve species descriptions in this figure.
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Fig. 2
Schematic diagram showing DNA-DNA hybridization procedure. (A) The DNA-DNA hybridization step. The DNA of two species of bacteria are heated and mixed together. During incubation, the DNA strands were dissociated and reannealed forming three kinds of hybrid double-stranded DNAs, (B) the melting procedure to analyze the melting profile of the hybridized DNA. The double-stranded DNA is bound to a column and the mixture is heated in small steps.
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References

1. Vandamme PAR. Murray PR, Baron EJ, editors. Taxonomy and Classification of Bacteria. Manual of Clinical Microbiology. 2007. 9th ed. Washington, DC: ASM Press;275–290.
2. Goodfellow M, O'Donnell AG. Handbook of New Bacterial Systematics. 1993. London: Academic Press.
3. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987. 37:463–464.
4. Young JM. Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol. 2001. 51:945–953.
5. Ursing JB, Rossellö-Mora RA, Garcia-Valdes E, Lalucat J. Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int J Syst Bacteriol. 1995. 45:604.
6. Colwell RR. Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol. 1970. 104:410–433.
7. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, et al. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis. 1998. 19:554–568.
8. Gupta RS. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev. 1998. 62:1435–1491.
9. Vancanneyt M, Vandamme P, Kersters K. Differentiation of Bordetella pertussis, B. parapertussis, and B. bronchiseptica by whole-cell protein electrophoresis and fatty acid analysis. Int J Syst Bacteriol. 1995. 45:843–847.
10. Willems A, Falsen E, Pot B, Jantzen E, Hoste B, Vandamme P, et al. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Bacteriol. 1990. 40:384–398.
11. Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J. Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev. 2005. 29:147–167.
12. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA. 2005. 102:2567–2572.
13. Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology. 2010. 100:208–215.
14. Schmid CW, Marks J. DNA hybridization as a guide to phylogeny: chemical and physical limits. J Mol Evol. 1990. 30:237–246.
15. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 1996. 60:407–438.
16. Krieg N, Garrity G. Boone DR, Castenholz RW, Garrity GM, editors. On Using the Manual. Bergey's Manual of Systematic Bacteriology. 2001. 2nd ed. New York: Springer-Verlag;15–19.
17. Ludwig J, Klenk H. Boone DR, Castenholz RW, editors. Overview: a Phylogenetic Backbone and Taxonomic Framework for Prokaryotic Systematics. Bergey's Manual of Systematic Bacteriology. 2001. New York: Springer-verlag;49–65.
18. Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995. 59:143–169.
19. Fox GE, Wisotzkey JD, Jurtshuk P Jr. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol. 1992. 42:166–170.
20. Stackebrandt E, Goebel B. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994. 44:846–849.
21. Clinical and Laboratory Standards Institute. Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline. MM18-A. 2008. Wayne, PA: Clinical and Laboratory Standards Institute.
22. Harrington CS, On SL. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. Int J Syst Bacteriol. 1999. 49:1171–1175.
23. Vandamme P, Harrington CS, Jalava K, On SL. Misidentifying helicobacters: the Helicobacter cinaedi example. J Clin Microbiol. 2000. 38:2261–2266.
24. Clayton RA, Sutton G, Hinkle PS Jr, Bult C, Fields C. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol. 1995. 45:595–599.
25. Jaspers E, Overmann J. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol. 2004. 70:4831–4839.
26. Sneath PHA. Krieg NR, Holt JG, editors. Numerical Taxonomy. Bergey's Manual of Systematic Bacteriology. 1984. 1st ed. Baltimore: The Williams & Wilkins Co.;111–118.
27. Sokal RR, Sneath PHA. Principles of Numerical Taxonomy. 1963. 1st ed. San Francisco: WH Freeman & Co..
28. Suzuki K, Goodfellow M, O'Donnell AG. Cell Envelopes and Classification. 1993. London: Academic Press.
29. Marvin LF, Roberts MA, Fay LB. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry. Clin Chim Acta. 2003. 337:11–21.
30. Zaluzec EJ, Gage DA, Watson JT. Matrix-assisted laser desorption ionization mass spectrometry: applications in peptide and protein characterization. Protein Expr Purif. 1995. 6:109–123.
31. Lay JO Jr. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev. 2001. 20:172–194.
32. Clarridge JE 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004. 17:840–862.
33. Fontana C, Favaro M, Pelliccioni M, Pistoia ES, Favalli C. Use of the MicroSeq 500 16S rRNA gene-based sequencing for identification of bacterial isolates that commercial automated systems failed to identify correctly. J Clin Microbiol. 2005. 43:615–619.
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