Use of subtractive hybridization to design habitat-based oligonucleotide probes for investigation of natural bacterial communities

Applied and Environmental Microbiology

Volumn 64, Issue 1, 1998, Pages 185-191

  Mau, Margit ^a   Timmis, Kenneth N ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA 16S;

ALCALIGENES FAECALIS; ARTICLE; BACTERIAL GENE; BACTERIUM COLONY; BACTERIUM IDENTIFICATION; BURKHOLDERIA; DNA RNA HYBRIDIZATION; NONHUMAN; RNA GENE;

ALCALIGENES FAECALIS; BACTERIA (MICROORGANISMS); BURKHOLDERIA; NEGIBACTERIA;

EID: 0031965210     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.1.185-191.1998     Document Type: Article

References (20)

1. Alm, E. W., D. B. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62:3557-3559.
2. Bjourson, A. J., and J. E. Cooper. 1988. Isolation of Rhizobium loti strain-specific DNA sequences by subtraction hybridization. Appl. Environ. Microbiol. 54:2852-2855.
3. Brosius, J., J. L. Palmer, H. P. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805.
4. Collins, M., E. F. Fritsch, M. S. Ellwood, S. E. Diamond, J. I. Williams, and J. G. Brewen. 1988. A novel diagnostic method based on DNA strand displacement. Mol. Cell Probes 2:15-30.
5. Darrasse, A., A. Kotoujanansky, and Y. Bertheau. 1994. Isolation by genomic subtraction of DNA probes specific for Erwinia carotovora subsp. atroseptica. Appl. Environ. Microbiol. 60:298-306.
6. Ellwood, M. S., M. M. Collins, E. F. Fritsch, J. I. Williams, S. E. Diamond, and J. G. Brewen. 1986. Strand displacement applied to assays with nucleic acid probes. Clin. Chem. 32:1631-1636.
7. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
8. Jaeger, J. A., D. H. Turner, and M. Zuker. 1990. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:281-306.
9. Lane, D. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, United Kingdom.
10. Maidak, B. J., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1996. The Ribosomal Database Project. Nucleic Acids Res. 24:82-85.
11. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K.-H. Schleifer. 1992. Phylogenetic oligonucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593-600.
12. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplancton communities. Limnol. Oceanogr. 40:148-158.
13. Rodriguez, I. R., and G. J. Chader. 1992. A novel method for the isolation of tissue-specific genes. Nucleic Acids Res. 20:3528.
14. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
15. Schnellbacher, I. 1995. Einsatz von phylogenetischen Sonden zur Untersuchung einer mikrobiellen Gemeinschaft in Elbe-Aufwuchs. Diploma thesis. Technical University of Braunschweig, Braunschweig, Germany.
16. Scott, M. R. D., K.-H. Westphal, and P. W. C. Rigby. 1983. Activation of mouse genes in transformed cells. Cell 34:557-567.
17. Stackebrandt, E., and F. A. Rainey. 1995. Partial and complete 16S rDNA sequences, their use in generation of 16S rEDNA phylogenetic trees and their implications in molecular ecological studies, p. 3.1.1. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruin (ed.). Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
18. Straus, D., and F. M. Ausubel. 1990. Genomic subtraction for cloning DNA corresponding to deletion mutations. Proc. Natl. Acad. Sci. USA 87:1889-1893.
19. Welcher, A. A., A. R. Torres, and D. C. Ward. 1986. Selective enrichment of specific DNA. cDNA and RNA sequences using biotinylated probes, avidin and copper-chelate agarose. Nucleic Acids Res. 24:10027-10044.
20. Wilson, K. 1987. Preparation of genomic DNA from bacteria, p. 2.4.1-2.4.5. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology. John Wiley & Sons, New York, N.Y.