1887

Chapter 2 : The Family : Taxonomic Considerations

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

The Family : Taxonomic Considerations, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817541/9781555813420_Chap02-1.gif /docserver/preview/fulltext/10.1128/9781555817541/9781555813420_Chap02-2.gif

Abstract:

This chapter provides an overview of taxonomic changes that have occurred within the family over the past 40 years and how these changes will impact our lives. This chapter is not meant to be a comprehensive review of bacterial taxonomy. It is hoped that it will provide the basic concepts and understanding of how genera and species evolve within the . Today, phenotypic methods employ a variety of methods in addition to traditional biochemical tests. These methods include colonial and microscopic morphology, chemotaxonomy (gas liquid chromatography), carbon utilization assays, phage typing, dye-element inhibitory tests, and serology. The use of molecular techniques to systematically study various groups of bacteria including the was in its infancy in the 1960s. In the 1970s, Don Brenner and his colleagues at the Centers for Disease Control and Prevention and the Walter Reed Army Institute of Research redefined genera and species within the family with their pioneering studies employing DNA-DNA hybridization assays. Two ribosomal oligonucleotide probes have been developed to rapidly detect members of the family . Both probes appear to have similar sensitivities and specificities and have been tested against a variety of nonenterobacterial species. Given the fact that all single techniques have inherent limitations, a more global approach would be the ideal method to study new taxa and to determine the correct taxonomic position of species within a family. Such a method has been proposed; the term polyphasic taxonomy has been coined for this consensus approach.

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2

Key Concept Ranking

16s rRNA Sequencing
0.6445034
Gram-Negative Bacteria
0.61310494
Molecular Techniques
0.4540809
Klebsiella ornithinolytica
0.44319353
0.6445034
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Schematic representation of steps in the process of the discovery and naming of a new bacterial species. The process starts in this figure (center) with the identification of bacteria in the clinical laboratory with unusual phenotypes.

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Growth in the number of genera and species in the family between 1972 and 2003. Data are from references 7 and 14 and from www.bacterio.cict.fr.

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Breakdown of genera in the family , based upon their major associations.

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817541.chap2
1. Achtman, M.,, K. Zurth,, G. Morelli,, G. Torres,, A. Guiyoule,, and E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:1404314048.
2. Ajithkumar, B.,, V. P. Ajithkumar,, R. Iriye,, Y. Doi,, and T. Sakai. 2003. Spore-forming Serratia marcescens subsp. sakuensis subsp. nov. isolated from a domestic wastewater treatment plant. Int. J. Syst. Evol. Microbiol. 53:253258.
3. Bohnert, J.,, B. Hübner,, and K. Botzenhart. 2000. Rapid identification of Enterobacteriaceae using a novel 23S rRNA-targeted oligonucleotide probe. Int. J. Hyg. Environ. Health 203: 7782.
4. Böttger, E. C.,, M. Jürs,, T. Barrett,, K. Wachsmuth,, S. Metzger,, and D. Bitter-Suermann. 1987. Qualitative and quantitative determination of enterobacterial common antigen (ECA) with monoclonal antibodies: expression of ECA by two Actinobacillus species. J. Clin. Microbiol. 25:377382.
5. Boye, K.,, and D. S. Hansen. 2003. Sequencing of 16S rDNA of Klebsiella: taxonomic relations within the genus and to other Enterobacteriaceae. Int. J. Med. Microbiol. 292: 495503.
6. Brenner, D. J. 1977. Characterization and clinical identification of Enterobacteriaceae by DNA hybridization. Prog. Clin. Pathol. 7:71117.
7. Brenner, D. J., 21 May 1999, posting date. Introduction to the family Enterobacteriaceae. In A. Balows,, H. G. Trüper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community, 2nd ed. [Online.] http://141.150.157.117:8080/prokPUB/index.htm. Springer-Verlag, New York, N.Y.
8. Brenner, D. J.,, G. R. Fanning,, C. V. Miklos,, and A. G. Steigerwalt. 1973. Polynucleotide sequence relatedness among Shigella species. Int. J. Syst. Bacteriol. 23:17.
9. Carter, J. S.,, F. J. Bowden,, I. Bastian,, G. M. Myers,, K. S. Sriprakash,, and D. J. Kemp. 1999. Phylogenetic evidence for reclassification of Calymmatobacterium granulomatis as Klebsiella granulomatis comb. nov. Int. J. Syst. Bacteriol. 49:16951700.
10. Christensen, H.,, M. Bisgaard,, W. Frederiksen,, R. Mutters,, P. Kuhnert,, and J. E. Olsen. 2001. Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify Recommendation 30b of the Bacteriological Code (1990 Revision). Int. J. Syst. Evol. Microbiol. 51:22212225.
11. Dauga, C. 2002. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecular for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52:531547.
12. Drancourt, M.,, C. Bollet,, A. Carlioz,, R. Mattelin,, J.-P. Gayral,, and D. Raoult. 2000. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38:36233630.
13. Drancourt, M.,, C. Bollet,, A. Carta,, and P. Rousselier. 2001. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int. J. Syst. Evol. Microbiol. 51:925932.
14. Farmer, J. J., III,, B. R. Davis,, F. W. Hickman-Brenner,, A. McWhorter,, G. P. Huntley-Carter,, M. A. Asbury,, C. Riddle,, H. G. Wathen-Grady,, C. Elias,, G. R. Fanning,, A. G. Steigerwalt,, C. M. O’Hara,, G. K. Morris,, P. B. Smith,, and D. J. Brenner. 1985. Biochemical identification of new species and biogroups of Enterobacteriaceae isolated from clinical specimens. J. Clin. Microbiol. 21:4676.
15. Gürtler, V.,, and B. C. Mayall. 2001. Genomic approaches to typing, taxonomy and evolution of bacterial isolates. Int. J. Syst. Evol. Microbiol. 51:316.
16. Hedegaard, J.,, S. A. D. A. Steffensen,, N. Nørskov-Lauritsen,, K. K. Mortensen,, and H. U. Sperling-Petersen. 1999. Identification of Enterobacteriaceae by partial sequencing of the gene encoding translation initiation factor 2. Int. J. Syst. Bacteriol. 49:15311538.
17. Janda, J. M.,, and S. L. Abbott. 2002. Bacterial identification for publication: when is enough enough? J. Clin. Microbiol. 40:18871891.
18. Johnson, J. R. 2000. Shigella and Escherichia coli at the crossroads: Machiavellian masqueraders or taxonomic treachery? J. Med. Microbiol. 49:583585.
19. Lan, R.,, and P. R. Reeves. 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9:419424.
20. Martinez-Murcia, A. J.,, S. Benlloch,, and M. D. Collins. 1992. Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridization. Int. J. Syst. Bacteriol. 42:412421.
21. Miller, J. M.,, and P. Alachi. 1996. Evaluation of a new computer-enhanced identification program for microorganisms: adaptation of BioBASE for identification of members of the family Enterobacteriaceae. J. Clin. Microbiol. 54: 179181.
22. Murray, R. G. E.,, and K. H. Schleifer. 1994. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol. 44:174176.
23. Ootsubo, M.,, T. Shimizu,, R. Tanaka,, T. Sawabe,, K. Tajima,, M. Yoshimizu,, Y. Ezura,, T. Ezaki,, and H. Oyaizu. 2002. Oligonucleotide probe for detecting Enterobacteriaceae by in situ hybridization. J. Appl. Microbiol. 93:6068.
24. Priest, F.,, and B. Austin. 1993. Modern bacterial taxonomy. Chapman & Hall, London, United Kingdom.
25. Rosselló-Mora, R.,, and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Lett. 25:3967.
26. Shieh, W. Y.,, and W. D. Jean. 1998. Alterococcus agarolyticus, gen. nov., sp. nov., a halophilic thermophilic bacterium capable of agar degradation. Can. J. Microbiol. 44:637645.
27. Sneath, P. H. A. (ed.). 1992. International Code of Nomenclature of Bacteria and Statutes of the International Committee on Systematic Bacteriology and Statutes of the Bacteriology and Applied Microbiology Section of the International Union of Microbiological Societies. American Society for Microbiology, Washington, D.C.
28. Stackebrandt, E.,, and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846849.
29. Tamas, I.,, L. Klasson,, B. Canbäck,, A. K. Näslund,, A.-S. Eriksson,, J. J. Wernegreen,, J. P. Sandström,, N. A. Moran,, and S. G. E. Andersson. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:23762379.
30. Vandamme, P.,, B. Pot,, M. Gillis,, P. De Vos,, K. Kersters,, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407438.
31. Warren, J. R.,, J. J. Farmer III,, F. E. Dewhirst,, K. Birkhead,, T. Zembower,, L. R. Peterson,, L. Sims,, and M. Bhattacharya. 2000. Outbreak of nosocomial infections due to extendedspectrum β-lactamase-producing strains of Enteric Group 137, a new member of the family Enterobacteriaceae closely related to Citrobacter farmeri and Citrobacter amalonaticus. J. Clin. Microbiol. 38:39463952.
32. Wayne, L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. I. Krichevsky,, L. H. Moore,, W. E. C. Moore,, R. G. E. Murray,, E. Stackebrandt,, M. P. Starr,, and H. G. Trüper. 1987. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol. 37:463464.
33. Wernegreen, J. J. 2002. Genome evolution in bacterial endosymbionts of insects. Nat. Rev. Genet. 3:850861.
34. Woo, P. C. Y.,, E. Y. L. Cheung,, K.-W. Leung,, and K.-Y. Yuen. 2001. Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species with ambiguous biochemical profile from a renal transplant recipient. Diagn. Microbiol. Infect. Dis. 39:8593.
35. Zreik, L.,, J. M. Bové,, and M. Garnier. 1998. Phylogenetic characterization of the bacterium-like organism associated with marginal chlorosis of strawberry and proposition of a Candidatus taxon for the organism, ‘Candidatus Phlomobacter fragariae.’ Int. J. Syst. Bacteriol. 48:257261.

Tables

Generic image for table
Table 1

Oligonucleotide probes to detect

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2
Generic image for table
Table 2.

Defining phenotypic criteria for inclusion in the family : exceptions to the rule

Citation: Janda J, Abbott S. 2006. The Family : Taxonomic Considerations, p 7-14. In The Enterobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817541.ch2

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error