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Chapter 5 : Approaches to Identification

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Abstract:

The classification can be a general-purpose classification designed to provide a comprehensive catalog of all bacteria, or it can be a special-purpose classification covering a restricted range of organisms that are found in a particular environment or possess particular properties. This chapter summarizes various approaches to identification of microorganisms with emphasis on prokaryotes. However, virtually all the methods can be adapted to microbial eukaryotes. Microorganisms can be analyzed at various levels to gain information suitable for constructing databases and effecting identification. Nucleic acid hybridization also offers identification possibilities; indeed, chromosomal DNA hybridization forms the basis of the generally accepted species definition in bacterial systematics. The genetic information is expressed as proteins. Electrophoretic analysis of whole-cell proteins has been an effective approach to classification and identification. Other cell components can be analyzed by a range of techniques applied to either whole cells or particular cell extracts. For example, cellular and membrane lipids can be profiled using gas chromatography (GC), or whole cells can be volatilized and the products detected by mass spectrometry (MS). Morphology and physiology are the classical levels at which most conventional identification is done. The presence or absence of particular enzymes or metabolic pathways are typically characterized using commercial kits, and, again, computerized databases can be developed to enable rapid identification. The chapter reviews the application of these various methods and the practicalities of using them in the context of environmental microbiology.

Citation: Priest F. 2004. Approaches to Identification, p 49-56. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch5

Key Concept Ranking

Environmental Microbiology
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Restriction Fragment Length Polymorphism
0.49381906
Bacterial Classification
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Figure 1

Arrayed bacterial rDNA clones on a nylon membrane hybridized with P-labeled DNA oligonucleotide probes. (A) The full set of 27 discriminating probes and reference probe 28, each hybridized to a common set of clones; (B) a single probe (discriminating probe 4) hybridized to all 1,536 soil rDNA clones used in the study. Analysis with all 27 probes produced a hybridization fingerprint for every clone (from Valinsky et al., 2002 with permission).

Citation: Priest F. 2004. Approaches to Identification, p 49-56. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch5
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References

/content/book/10.1128/9781555817770.chap5
1. Amann, R.,, and W. Ludwig. 2000. Ribosomal RNA-targeted nucleic acid probes for studies of microbial ecology. FEMS Microbiol. Rev. 24:555565.
2. Amann, R. I.,, W. Ludwig,, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143169.
3. Aquino de Muro, M.,, and F. G. Priest. 1994. A colony hybridization procedure for the identification of mosquitocidal strains of Bacillus sphaericus on isolation plates. J. Invertebr. Pathol. 63:310333.
4. Baldus Patel, J.,, D. G. B. Leonard,, X. Pan,, J. M. Musser,, R. E. Berman,, and I. Nachamkin. 2000. Sequence-based identification of Mycobacterium species using the Microseq 500 16S rDNA bacterial identification system. J. Clin. Microbiol. 38: 246251.
5. Barney, M.,, A. Volgyi,, A. Navarro,, and D. Ryder. 2001. Ribo-printing and 16S rRNA gene sequencing for identification of brewery Pediococcus isolates. Appl. Environ. Microbiol. 67: 553560.
6. Behr, T.,, C. Koob,, M. Schedl,, A. Mehlen,, H. Meier,, D. Knopp,, E. Frahm,, U. Obst,, K. H. Schleifer,, R. Niessner,, and W. Ludwig. 2000. A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization. Syst. App. Microbiol. 23:563572.
7. Cappa, F.,, and P. S. Cocconcelli. 2001. Identification of fungi from dairy products by means of 18S rRNA analysis. Int. J. Food Microbiol. 69:157160.
8. Carpenter Boggs, L.,, A. C. Kennedy,, and J. P. Reganold. 1998. Use of phospholipid fatty acids and carbon source utilization to track microbial community succession in developing compost. Appl. Environ. Microbiol. 64:40624064.
9. Connolly, G. R.,, and B. K. C. Patel. 2002. Development of fluorescent adjacent hybridization probes and their application in real-time PCR for the simultaneous detection and identification of Fervidobacterium and Caloramator. Int. J. Syst. Evol. Microbiol. 52:18371843.
10. Cowan, S. T. 1965. Principles and practice of bacterial taxonomy. J. Gen. Microbiol. 39:143155.
11. Daane, L. L.,, I. Harjono,, G. J. Zylstra,, and M. M. Haggblom. 2001. Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants. Appl. Environ. Microbiol. 67:26832691.
12. De Cesare, A.,, and G. Manfreda. 2002. Use of the automated ribotyping for epidemiological investigations. Ann. Microbiol. 52:181190.
13. Drancourt, M.,, C. Bollet,, A. Carlioz,, R. Martelin,, J.-P. Gayral,, and D. Raoult. 2000. 16S ribosmal sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38:36233630.
14. Ellerbrook, H.,, H. Nattermann,, M. Ozel,, I. Beutin,, B. Appel,, and G. Pauli. 2002. Rapid and sensitive identification of pathogenic and apathogenic Bacillus anthracis by real-time PCR. FEMS Microbiol. Lett. 214:5159.
15. Goodacre, R.,, E. M. Timmins,, R. Burton,, N. Kaderbhai,, A. M. Woodward,, D. B. Kell,, and P. J. Rooney. 1998. Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144:11571170.
16. Goto, K.,, T. Omura,, Y. Hara,, and Y. Sadaie. 2000. Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J. Gen. Appl. Microbiol. 46:18.
17. Ibekwe, A. M.,, and A. C. Kennedy. 1998. Phospholipid fatty acid profiles and carbon utilization patterns for analysis of microbial community structure under field and greenhouse conditions. FEMS Microbiol. Ecol. 26:151163.
18. Jarvis, B. D. W.,, S. Sivakumaran,, S. W. Tighe,, and M. Gillis. 1996. Identification of Agrobacterium and Rhizobium species based on cellular fatty acid composition. Plant Soil 184:143158.
19. Lay, J. O. 2001. MALDI-TOF-MS of bacteria. Mass Spectrom. Rev. 20:172194.
20. Liu, W. T.,, A. D. Mirzabekov,, and D. A. Stahl. 2001. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 3:619629.
21. Logan, J. M. J.,, K. J. Edwards,, N. A. Saunders,, and J. Stanley. 2001. Rapid identification of Campylobacter spp. by melting peak analysis of biprobes in real-time PCR. J. Clin. Microbiol. 39:22272232.
22. Loy, A.,, A. Lehner,, N. Lee,, J. Adamczyk,, H. Meier,, J. Ernst,, K.-H. Schleifer,, and M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes on the environment. Appl. Environ. Microbiol. 68:50645081.
23. Maidak, B. L.,, J. R. Cole,, T. G. Lilburn,, C. T. J. Parker,, P. R. Saxman,, P. J. Farris,, G. M. Garrity,, G. J. Olsen,, T. M. Schmidt,, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:8285.
24. Mygind, T.,, S. Birklund,, E. Falk,, and G. Christiansen. 2001. Evaluation of real-time quantitative PCR for identification and quantification of Chlamydia pneumoniae by comparison with immunohistochemistry. J. Microbiol. Methods. 46:241251.
25. Obereuter, H.,, H. J. Charzinski,, and S. Scherer. 2002. Identification of coryneform bacteria and related taxa by Fourier transform infrared spectroscopy (FT-IR). Int. J. Syst. Evol. Microbiol. 52:91100.
26. Pot, B.,, P. Vandamme,, and K. Kersters,. 1994. Analysis of electrophorestic whole organisms fingerprints, p. 493521. In M. Goodfellow, and A. G. O'Donnell (ed.), Chemical Methods in Prokaryotic Systematics. Wiley, Chichester, United Kingdom.
27. Roberts, M. S.,, L. K. Nakamura,, and F. M. Cohan. 1994. Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence and differences in fatty acid composition. Int. J. Syst. Bacteriol. 44:256264.
28. Simpson, K. L.,, B. Pettersson,, and F. G. Priest. 2001. Characterization of lactobacilli from Scotch malt whisky distilleries and description of Lactobacillus ferintoshensis sp. nov., a new species isolated from malt whisky fermentations. Microbiology 147:10071016.
29. Stahl, D. A. 1995. Application of phylogenetically based hybridization probes to microbial ecology. Mol. Ecol. 4:535542.
30. Tang, Y.-W.,, A. Von Graevenitz,, M. G. Waddington,, M. K. Hopkins,, D. H. Smith,, H. Li,, C. P. Kolbert,, S. O. Montbomery,, and D. H. Persing. 2000. Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J. Clin. Microbiol. 38:16761678.
31. Timmins, E. M.,, D. E. Quain,, and R. Goodacre. 1998a. Differentiation of brewing yeast strains by pyrolysis mass spectrometry and Fourier transform infrared spectroscopy. Yeast 14:885893.
32. Timmins, E. M.,, S. A. Howell,, B. K. Alsberg,, W. C. Noble,, and R. Goodacre. 1998b. Rapid differentiation of closely related Candida species and strains using pyrolysis-mass spectrometry and Fourier transform-infrared spectroscopy. J. Clin. Microbiol. 36:367374.
33. Trotha, R.,, T. Hanck,, W. König,, and B. König. 2001. Rapid ribosequencing—an effective diagnostic tool for detecting microbial infection. Infection 29:1216.
34. Unnerstad, H.,, H. Ericsson,, A. Alderborn,, W. Tham,, M.-L. Danielsson-Tham,, and J. G. Mattsson. 2001. Pyrosequencing as a method for grouping of Listeria monocytogenes strains on the basis of single-nucleotide polymorphisms. Appl. Environ. Microbiol. 67:53395342.
35. Vaidyanathan, S.,, J. J. Rowland,, D. B. Kell,, and R. Goodacre. 2001. Discrimination of aerobic endospore-forming bacteria via electrospray-ionization mass spectrometry of whole cell suspensions. Anal. Chem. 73:41344144.
36. Valente, P.,, J. Ramos,, and O. Leoncini. 1999. Sequencing as a tool in yeast molecular taxonomy. Can. ]. Microbiol. 45:949958.
37. Valinsky, L.,, G. Delia Vedova,, A. J. Scupham,, S. Alvey,, A. Figueroa,, B. Yin,, J. Hartin,, M. Chroback,, D. E. Crowley,, T. Jiang,, and J. Borneman. 2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68:32433250.
38. Van Baar, B. L. 2000. Characterization of bacteria by matrix assisted laser desorption/ionisationand electrospray mass spectrometry. FEMS Microbiol. Rev. 24:193219.
39. 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.
40. Vaneechoutte, M. 1996. DNA fingerprinting techniques for microorganisms; a proposal for classification and nomenclature. Mol. Biotechnol. 6:115142.
41. von Wintzingerode, F.,, S. Bocker,, C. Schlotelburg,, N. H. L. Chiu,, N. Storm,, C. Jurinke,, C. R. Cantor,, U. B. Gobel,, and D. van den Boom. 2002. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc. Natl. Acad. Set. USA 99:70397044.
42. Voordouw, G.,, J. K. Voordouw,, R. R. Karkhoff-Schweizer,, P. M. Fedorak,, and D. W. S. Westlake. 1991. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl. Environ. Microbiol. 57:30703078.
43. Wang, R.-F.,, M. L. Beggs,, L. H. Robertson,, and C. E. Cerniglia. 2002. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213:175182.
44. Wayne, L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. I. Krichevsky,, W. F. 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.
45. Wenning, M.,, H. Seiler,, and S. Scherer. 2002. Fourier-transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Appl. Environ. Microbiol. 68:47174721.
46. Wilson, K. H.,, W. J. Wilson,, J. L. Radosevich,, T. Z. DeSantis,, V. S. Viswanathan,, T. A. Kuczmarski,, and G. L. Andersen. 2002. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68:25352541.

Tables

Generic image for table
Table 1

Features of some whole-cell fingerprinting methods

Citation: Priest F. 2004. Approaches to Identification, p 49-56. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch5

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