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Chapter 21 : What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?

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What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, Page 1 of 2

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Abstract:

This chapter briefly introduces the presently recommended criteria for establishing species relationships for bacteria. The author surveys the methods that have been used for identifying and classifying prokaryotes, highlighting the ways in which these methods have been used to help construct a definition of a bacterial species. Since sequence analysis of molecules, in particular, 16S rRNA, is providing a powerful phylogenetic framework for the classification of organisms, the author discusses the methods involved in molecular sequence analysis. The advantages and limitations in using 16S rRNA sequence analysis in taxonomie studies and the importance of including analyses of other gene sequences in bacterial species circumscription are discussed and explored. The 16S rRNA molecule of bacteria has been used extensively for phylogenetic analysis. It allows a wide range of discrimination among organisms, and, within the expected range of resolution for various methods, there is generally a good agreement between relationships obtained using other taxonomic methods and those obtained using 16S rRNA analysis. It was recognized that there are some very promising new genomic technologies that should be further developed to help define inter- and intraspecies relationships, including sequence analysis of various housekeeping genes and DNA-typing methods, as well as DNA arrays and other technologies that take advantage of whole-genome sequence data.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21

Key Concept Ranking

Microbial Ecology
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Restriction Fragment Length Polymorphism
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Figures

Image of FIGURE 1
FIGURE 1

Example of the use of a series of classical phenotypic tests to identify an unknown organism. The example shown here shows the procedures that could be used to differentiate among several gram-positive cocci.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 2
FIGURE 2

The method of numerical taxonomy. A simple example is given in which three organisms are compared.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 3
FIGURE 3

Overview of the steps involved in a typical DNA-DNA hybridization assay.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 4
FIGURE 4

Thermal denaturation profiles of two hypothetical duplex DNA samples, one a heteroduplex of DNA from two different organisms, the other a homoduplex of DNA from one of the organisms hybridized to itself. The of both samples is indicated, as is the Δ

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 5
FIGURE 5

Efficacy of resolution by various taxonomie methods. Information is adapted from .

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 6
FIGURE 6

Conservation of regions in the 16S rRNA primary sequence and use of the conserved sequences and secondary structure to facilitate alignment of 16S rRNA sequences. Figure is reprinted from ( ) with permission from the publisher. (A) Diagram of the secondary structure of the 16S rRNA molecule from . Line thickness indicates the level of conservation of various regions of the primary sequence. The thick lines indicate regions of nearly universal conservation, thin lines indicate regions with an intermediate level of conservation, and dashed lines indicate hypervariable regions. (?) The 16S rRNA sequence obtained from an Octopus Spring cyanobacterial mat sample superimposed on the 16S rRNA secondary structure. Arrowheads indicate the nucleotides that differ from the sequence. Features that characterize the sequence as being from a cyanobacterium are indicated with lines (primary structure features) or asterisks (secondary structure features).

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 7
FIGURE 7

Phylogenetic trees based on 16S rRNA gene and partial gene sequences from 20 enteric strains. The figure is reproduced from ( ) with permission of the publisher. The trees are those obtained from DNA maximum likelihood analyses with a molecular clock using as an outgroup. Asterisks indicate nodes with bootstrap values >90%, and the thick lines indicate topologies that are conserved in analyses using neighbor joining from Jukes and Cantor DNA distance matrix and DNA parsimony.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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Image of FIGURE 8
FIGURE 8

Diagram indicating the major categories of the many pieces of taxonomie data that are used to ultimately form a consensus classification using a polyphasic taxonomie approach.

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
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References

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1. Cohan, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50:513524.
2. Fox, G. E.,, J. D. Wisotzkey,, and J. P. Jurtshuk. 1992. How close is close: rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166170.
3. Maiden, M. C. J.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russel,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman,, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic organisms. Proc. Natl. Acad. Sri. USA 95: 31403145.
4. Mollet, C.,, M. Drancourt,, and D. Raoult. 1997. rpoB sequence analysis as a novel basis for bacterial identification. Mol. Microbiol. 26:10051011.
5. Stackebrandt, E.,, and B. M. Goebel. 1994. Taxonomie 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.
6. Vandamme, P.,, B. Pot,, M. Gillis,, P. D. Vos,, K. Kersters,, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial system-atics. Micobiol. Rev. 60:407438.
7. Vulic, M.,, F. Dionisio,, F. Taddei,, and M. Radman. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Set. USA 94:97639767.
8. Ward, D. M.,, M. M. Bateson,, and R. Weller,. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature, p. 219286. In K. C. Marshall (ed.), Advances in Microbial Ecology, vol. 12. Plenum Press, New York, N.Y.
9. Brenner, D.J.,, J. T. Staley,, and N. K. Krieg,. 2001. Classification of prokaryotic organisms and the concept of a bacterial species, p. 2731. In D. R. Boone,, R. W. Castenholz,, and G. M. Garrity (ed.), Bergey's Manual of Systematic Bacteriology, 2nd ed. Springer, New York, N.Y.
10. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457487.
11. Goodfellow, M.,, G. P. Manfio,, and J. Chun,. 1997. Towards a practical species concept for cultivable bacteria, p. 2559. In M. F. Claridge,, H. A. Dawah,, and M. R. Wilson (ed.), Species: The Units of Biodiversity. Chapman & Hall, London, United Kingdom.
12. Rosselló-Mora, R.,, and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 21:3967.
13. Stackebrandt, E.,, W. Frederiksen,, G. M. Garrity,, P. A. D. Grimont,, P. Kâmpfer,, M. C. J. Maiden,, X. Nesme,, R. Rosselló-Mora,, J. Swings,, H. G. Triiper,, L. Vauterin,, A. C. Ward,, and W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52:10431047.
14. Vandamme, P.,, B. Pot,, M. Gillis,, P. de Vos,, K. Kersters,, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial system-atics. Microbiol. Rev. 60:407438.
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Tables

Generic image for table
TABLE 1

Considerations in choosing a phylogenetic marker molecule

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21
Generic image for table
TABLE 2

Alternative phylogenetic molecular markers

Citation: van Waasbergen L. 2004. What Makes a Bacterial Species? When Molecular Sequence Data Are Used, Is rRNA Enough?, p 339-356. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch21

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