1887

Abstract

Small-subunit rRNA (SSU rRNA) sequencing is a powerful tool to detect, identify, and classify prokaryotic organisms, and there is currently an explosion of SSU rRNA sequencing in the microbiology community. We report unexpectedly high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank. A total of 82% of the prokaryote species with two published SSU rRNA sequences had more variable positions than a 0.1% random sequencing error would predict, and 48% of these sequence pairs had more variable positions than predicted by a 1.0% random sequencing error. Other sources of sequence variability must account for some of this intraspecific variation. Given these results, phylogenetic studies and biodiversity estimates obtained by using prokaryotic SSU rRNA sequences cannot proceed under the assumption that rRNA sequences of single operons from single isolates adequately represent their taxa. Sequencing SSU rRNA molecules from multiple operons and multiple isolates is highly recommended to obtain meaningful phylogenetic hypotheses, as is careful attention to accurate strain identification.

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1995-07-01
2024-12-10
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References

  1. Adams M. D., Kerlavage A. R., Fields C., Venter J. C. 1993; 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genet. 4:256–267
    [Google Scholar]
  2. Amann R., Ludwig W., Schleifer K.-H. 1994; Identification of uncultured bacteria: a challenging task for molecular taxonomists. ASM News 60:360–365
    [Google Scholar]
  3. Aquino de Muro M., Priest F. G. 1993; Phylogenetic analysis of Bacillus sphaericus and development of an oligonucleotide probe specific for mosquito-pathogenic strains. FEMS Microbiol. Lett. 112:205–210
    [Google Scholar]
  4. Baranton G., Postic D., Saint Girons I., Boerlin P., Piffaretti J.-C., Assous M., Grimont P. A. D. 1992; Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS4161 associated with Lyme borreliosis. Int. J. Syst. Bacteriol. 42:378–383
    [Google Scholar]
  5. Barns S. M., Fundyga R. E., Jeffries M. W., Pace N. R. 1994; Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci.USA 91:1609–1613
    [Google Scholar]
  6. Baylis H. A., Bibb M. J. 1987; The nucleotide sequence of a 16S rRNA gene from Streptomyces coelicolor A3(2). Nucleic Acids Res. 15:7176
    [Google Scholar]
  7. Clark A. G., Whittam T. S. 1992; Sequencing errors and molecular evolutionary analysis. Mol. Biol. Evol. 9:744–752
    [Google Scholar]
  8. Dryden S. C., Kaplan S. 1990; Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides . Nucleic Acids Res. 18:7267–7277
    [Google Scholar]
  9. Fell J. W., Statzell-Tallman A., Lutz M. J., Kurtzman C. P. 1992; Partial rRNA sequences in marine yeasts: a model for identification of marine eukaryotes. Mol. Mar. Biol. Biotechnol. 1:175–186
    [Google Scholar]
  10. Felsenstein J. 1993; PHYLIP, version 3.5. University of Washington; Seattle:
    [Google Scholar]
  11. Field K. G., Landfear S. M., Giovannoni S. J. 1991; 18S rRNA sequences of Leishmania enriettii promastigore and amastigote. Int. J. Parasitol. 21:483–485
    [Google Scholar]
  12. Fox G. E., Wisotzkey J. D., Jurtshuk P. 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166–170
    [Google Scholar]
  13. Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. 1990; Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345:60–63
    [Google Scholar]
  14. Haygood M. G., Distel D. L. 1993; Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio . Nature (London) 363:154–156
    [Google Scholar]
  15. Hillis D. M., Dixon M. T. 1991; Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411–453
    [Google Scholar]
  16. Kurtzman C. P. 1992; rRNA sequence comparison for assessing phylogenetic relationships among yeasts. Int. J. Syst. Bacteriol. 42:1–6
    [Google Scholar]
  17. Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. 1993; The Ribosomal Database Project. Nucleic Acids Res 21: Suppl 3021–3023
    [Google Scholar]
  18. Marconi R. T., Garon C. F. 1992; Phylogenetic analysis of the genus Borrelia: a comparison of North American and European isolates of Borrelia burgdorferi . J. Bacteriol. 174:241–244
    [Google Scholar]
  19. Mevarech M., Hirsch-Twizer S., Goldman S., Yakobson E., Eisenberg H., Dennis P. P. 1989; Isolation and characterization of the rRNA gene clusters of Halobacterium marismortui . J. Bacteriol. 171:3479–3485
    [Google Scholar]
  20. Mylvaganam S., Dennis P. P. 1992; Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui . Genetics 130:399–410
    [Google Scholar]
  21. Nakagawa Y., Yamasato K. 1993; Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J. Gen. Microbiol. 139:1155–1161
    [Google Scholar]
  22. Olsen G. L., Woese C. R., Overbeek R. 1994; The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1–6
    [Google Scholar]
  23. Ruimy R., Breittmayer V., Elbaze P., Lafay B., Boussemart O., Gauthier M., Christen R. 1994; Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences. Int. J. Syst. Bacteriol. 44:416–426
    [Google Scholar]
  24. Smith S. Unpublished data
  25. Sutton G. Unpublished data
  26. Swofford D. L. 1991; PAUP: phylogenetic analysis using parsimony, version 3.1. Illinois Natural History Survey; Champaign:
    [Google Scholar]
  27. van Wezel G. P., Vjgenboom E., Bosch L. 1991; A comparative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rrnA. Nucleic Acids Res. 19:4399–4403
    [Google Scholar]
  28. Ward D. M., Weller R., Bateson M. M. 1990; 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345:63–65
    [Google Scholar]
  29. Woese C. R. 1994; There must be a prokaryote somewhere: microbiology’s search for itself. Microbiol. Rev. 58:1–9
    [Google Scholar]
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