Abstract
Analysis of restriction fragment length polymorphism of bacterial small-subunit (SSU) rRNA sequences represents a potential means for characterizing complex bacterial populations such as those found in natural environments. In order to estimate the resolution potential of this approach, we have examined the SSU rRNA sequences in the Ribosomal Database Project bank using a computer algorithm which simulates hybridization between DNA sequences. Simulated hybridizations between a primer or probe sequence and an SSU rRNA sequence yield a value for each potential hybridization. This algorithm has been used to evaluate sites for PCR primers and hybridization probes used for classifying SSU rRNA sequences. Our analysis indicates that length variation in terminal restriction fragments of PCR products from the SSU rRNA sequences can identify a wide spectrum of bacteria. We also observe that the majority of restriction fragment length variation is the result of insertions and deletions rather than restriction site polymorphisms. This approach is also used to evaluate the relative efficiency and specificity of a number of published hybridization probes.
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- Amann R. I., Ludwig W., Schleifer K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995 Mar;59(1):143–169. doi: 10.1128/mr.59.1.143-169.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Avaniss-Aghajani E., Jones K., Chapman D., Brunk C. A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques. 1994 Jul;17(1):144-6, 148-9. [PubMed] [Google Scholar]
- Avaniss-Aghajani E., Jones K., Holtzman A., Aronson T., Glover N., Boian M., Froman S., Brunk C. F. Molecular technique for rapid identification of mycobacteria. J Clin Microbiol. 1996 Jan;34(1):98–102. doi: 10.1128/jcm.34.1.98-102.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Baldino F., Jr, Chesselet M. F., Lewis M. E. High-resolution in situ hybridization histochemistry. Methods Enzymol. 1989;168:761–777. doi: 10.1016/0076-6879(89)68057-3. [DOI] [PubMed] [Google Scholar]
- Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- DeLong E. F. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685–5689. doi: 10.1073/pnas.89.12.5685. [DOI] [PMC free article] [PubMed] [Google Scholar]
- DeLong E. F., Wu K. Y., Prézelin B. B., Jovine R. V. High abundance of Archaea in Antarctic marine picoplankton. Nature. 1994 Oct 20;371(6499):695–697. doi: 10.1038/371695a0. [DOI] [PubMed] [Google Scholar]
- Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fuhrman J. A., McCallum K., Davis A. A. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 1993 May;59(5):1294–1302. doi: 10.1128/aem.59.5.1294-1302.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. doi: 10.1038/345060a0. [DOI] [PubMed] [Google Scholar]
- Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. The ribosomal database project. Nucleic Acids Res. 1993 Jul 1;21(13):3021–3023. doi: 10.1093/nar/21.13.3021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moyer C. L., Dobbs F. C., Karl D. M. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol. 1994 Mar;60(3):871–879. doi: 10.1128/aem.60.3.871-879.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6. [DOI] [PubMed] [Google Scholar]
- Picard C., Ponsonnet C., Paget E., Nesme X., Simonet P. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol. 1992 Sep;58(9):2717–2722. doi: 10.1128/aem.58.9.2717-2722.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Raskin L., Stromley J. M., Rittmann B. E., Stahl D. A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol. 1994 Apr;60(4):1232–1240. doi: 10.1128/aem.60.4.1232-1240.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schmidt T. M., DeLong E. F., Pace N. R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991 Jul;173(14):4371–4378. doi: 10.1128/jb.173.14.4371-4378.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sogin M. L., Gunderson J. H. Structural diversity of eukaryotic small subunit ribosomal RNAs. Evolutionary implications. Ann N Y Acad Sci. 1987;503:125–139. doi: 10.1111/j.1749-6632.1987.tb40603.x. [DOI] [PubMed] [Google Scholar]
- Spaepen M., Angulo A. F., Marynen P., Cassiman J. J. Detection of bacterial and mycoplasma contamination in cell cultures by polymerase chain reaction. FEMS Microbiol Lett. 1992 Nov 15;78(1):89–94. doi: 10.1016/0378-1097(92)90293-w. [DOI] [PubMed] [Google Scholar]
- Stahl D. A., Lane D. J., Olsen G. J., Pace N. R. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol. 1985 Jun;49(6):1379–1384. doi: 10.1128/aem.49.6.1379-1384.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Steffan R. J., Atlas R. M. Polymerase chain reaction: applications in environmental microbiology. Annu Rev Microbiol. 1991;45:137–161. doi: 10.1146/annurev.mi.45.100191.001033. [DOI] [PubMed] [Google Scholar]
- Wang R. F., Cao W. W., Johnson M. G. 16S rRNA-based probes and polymerase chain reaction method to detect Listeria monocytogenes cells added to foods. Appl Environ Microbiol. 1992 Sep;58(9):2827–2831. doi: 10.1128/aem.58.9.2827-2831.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ward D. M., Weller R., Bateson M. M. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 1990 May 3;345(6270):63–65. doi: 10.1038/345063a0. [DOI] [PubMed] [Google Scholar]