Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy

Journal of Microbiological Methods

Volumn 26, Issue 3, 1996, Pages 247-259

  Heyndrickx, M ^a   Vauterin, L ^a   Vandamme, P ^a   Kersters, K ^a   De Vos, P ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

16S rDNA; Alcaligenes; ARDRA; Bacillus; Bordetella; genomic fingerprinting

Indexed keywords

RIBOSOME DNA;

ARTICLE; BACILLUS; BORDETELLA; CONTROLLED STUDY; DNA FINGERPRINTING; METHODOLOGY; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RIBOSOME; STANDARDIZATION; TAXONOMY;

ALCALIGENES; BACTERIA (MICROORGANISMS); BORDETELLA; PAENIBACILLUS; PAENIBACILLUS LAUTUS;

EID: 0030220506     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/0167-7012(96)00916-5     Document Type: Article

References (33)

1. [1] Woese, C. (1987) Bacterial evolution. Microbiol. Rev. 51, 221-271.
2. [2] Weisburg, W.G., Barns, S.M., Pelletier, D.A. and Lane, D.L. (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697-703.
3. [3] Maidak, B.L., Olsen, G.J., Larsen, N., Overbeek, R., McCaughey, M.J. and Woese, C.R. (1996) The ribosomal database project (RDP). Nucleic Acids Res. 24, 82-85.
4. [4] Ash, C., Farrow, J.A.E., Wallbanks, S. and Collins, M.D. (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett. Appl. Microbiol. 13, 202-206.
5. [5] Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai. J., Hippe, H. and Farrow, J.A.E. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812-826.
6. [6] Nei, M. and Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269-5273.
7. [7] Gurtler, V., Wilson, V.A. and Mayall, B.C. (1991) Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J. Gen. Microbiol. 137, 2673-2679.
8. [8] Jayaro, B.M., Doré Jr., J.J.E., Baumbach, G.A., Matthews, K.R. and Oliver, S.P. (1991) Differentiation of Streptococcus uberis from Streptococcus parauberis by polymerase chain reaction and restriction fragment length polymorphism analysis of 16S ribosomal DNA. J. Clin. Microbiol. 29, 2774-2778.
9. [9] Vaneechoutte, M., De Beenhouwer, H., Claeys, G., Verschraegen, G., De Rouck, A., Paepe, N., Elaichouni, A. and Portaels, F. (1993) Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J. Clin. Microbiol. 31, 2061-2065.
10. [10] Hughes, M.S., Skuce, R.A., Beck, L.-A. and Neill, S.D. (1993) Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences. J. Clin. Microbiol. 31, 3216-3222.
11. [11] Jannes, G., Vaneechoutte, M., Lannoo, M., Gillis, M., Vancanneyt, M., Vandamme, P., Verschraegen, G., Van Heuverswyn, H. and Rossau, R. (1993) Polyphasic taxonomy leading to the proposal of Moraxella canis sp. nov. for Moraxella catarrhalis-like strains. Int. J. Syst. Bacteriol. 43, 438-449.
12. [12] Ralph, D., McClelland, M., Welsh, J., Baranton, G. and Perolat, P. (1993) Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rRNA genes. J. Bacteriol. 175, 973-981.
13. [13] Laguerre, G., Allard, M.-R., Revoy, F. and Amarger, N. (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 60, 56-63.
14. [14] Carlotti, A. and Funke, G. (1994) Rapid distinction of Brevibacterium species by restriction analysis of rDNA generated by polymerase chain reaction. Syst. Appl. Microbiol. 17, 380-386.
15. [15] Vaneechoutte, M., Dijkshoorn, L., Tjernberg, I., Elaichouni, A., De Vos, P., Claeys, G. and Verschraegen, G. (1995) Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J. Clin. Microbiol. 33, 11-15.
16. [16] Nesme, X., Vaneechoutte, M., Orso, S., Hoste, B. and Swings, J. 1995. Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR-amplified 16S rRNA gene. Syst. Appl. Microbiol. 18, 127-135.
17. [17] Wilson, M.J., Wade, W.G. and Weightman, A.J. (1995) Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of human Capnocytophaga. J. Appl. Bacteriol. 78, 394-401.
18. [18] Pitcher, D.G., Saunders, N.A. and Owen, R.J. (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8, 151-156.
19. [19] Vandamme, P., Hommez, J., Vancanneyt, M., Monsieurs, M., Hoste, B., Cookson, B., Wirsing von König, C.H., Kersters, K. and Blackall, P.J. (1995) Bordetella hinzii sp. nov., isolated from poultry and humans. Int. J. Syst. Bacteriol. 45, 37-45.
20. [20] Vauterin, L. and Vauterin, P. (1992) Computer aided objective comparison of electrophoresis patterns for grouping and identification of microorganisms. Eur. Microbiol. 1, 37-41.
21. [21] De Ley, J., Segers, P., Kersters, K., Mannheim, W. and Lievens, A. (1986) Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family, Alcaligenaceae. Int. J. Syst. Bacteriol. 36, 405-414.
22. [22] Weyant, R.S., Hollis, D.G., Weaver, R.E., Amin, M.F.M., Steigerwalt, A.G., O'Connor, S.P., Whitney, A.M., Daneshvar, M.I., Moss, C.W. and Brenner, D.J. (1995) Bordetella holmesii sp. nov., a new Gram-negative species associated with septicemia. J. Clin. Microbiol. 33, 1-7.
23. [23] Kiredjian, M., Holmes, B., Kersters, K., Guilvout, I. and De Ley, J. (1986) Alcaligenes piechaudii, a new species from human clinical specimens and the environment. Int. J. Syst. Bacteriol. 36, 282-287.
24. [24] Kloos, W.E., Mohapatra, N., Dobrogosz, W., Ezzell, J.W. and Manclark, C.R. (1981) Deoxyribonucleotide sequence relationships among Bordetella species. Int. J. Syst. Bacteriol. 31, 173-176.
25. [25] Ash, C., Priest, F.G. and Collins, M.D. (1993) Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 64, 253-260.
26. [26] Rössler, D., Ludwig, W., Schleifer, K.H., Lin, C., McGill, T.J., Wisotzkey, J.D., Jurtschuk Jr., P. and Fox, G.E. (1991) Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies. Syst. Appl. Microbiol. 14, 266-269.
27. [27] Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P., Hoste, B., Kersters, K., De Vos, P., Logan, N.A., Aziz, A.M., Ali, N. and Berkeley, R.C.W. (1995) Paenibacillus (formerly Bacillus) gordonue (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus. Int. J. Syst. Bacteriol. 45, 661-669.
28. [28] Nakamura, L.K. and Swezey, J. (1983) Taxonomy of Bacillus circulans Jordan 1890: base composition and reassociation of deoxyribonucleic acid. Int. J. Syst. Bacteriol. 33, 46-52.
29. [29] Nakamura, L.K. and Swezey, J. (1983) Deoxyribonucleic acid relatedness of Bacillus circulans Jordan 1890 strains. Int. J. Syst. Bacteriol. 33, 703-708.
30. [30] Nakamura, L.K. (1984) Bacillus amylolyticus sp. nov., nom. rev., Bacillus lautus sp. nov., nom. rev., Bacillus pabuli sp. nov., nom. rev., and Bacillus validus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 34, 224-226.
31. [31] Stewart, G.C., Wilson, F.E. and Bott, K.F. (1982) Detailed physical mapping of the ribosomal RNA genes of Bacillus subtilis. Gene 19, 153-162.
32. [32] Clayton, R.A., Sutton, G., Hinkle Jr., P.S., Bult, C. and Fields, C. (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45, 595-599.
33. [33] Martin, F., Vairelles, D. and Henrion, B. (1993) Automated ribosomal DNA fingerprinting by capillary electrophoresis of PCR products. Anal. Biochem. 214, 182-189.