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. 1997 Jun;63(6):2338–2346. doi: 10.1128/aem.63.6.2338-2346.1997

A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations.

G A Komatsoulis 1, M S Waterman 1
PMCID: PMC168526  PMID: 9172353

Abstract

A new computational method (chimeric alignment) has been developed to detect chimeric 16S rRNA artifacts generated during PCR amplification from mixed bacterial populations. In contrast to other nearest-neighbor methods (e.g., CHECK_CHIMERA) that define sequence similarity by k-tuple matching, the chimeric alignment method uses the score from dynamic programming alignments. Further, the chimeric alignments are displayed to the user to assist in sequence classification. The distribution of improvement scores for 500 authentic, nonchimeric sequences and 300 artificial chimeras (constructed from authentic sequences) was used to study the sensitivity and accuracy of both chimeric alignment and CHECK_CHIMERA. At a constant rate of authentic sequence misclassification (5%), chimeric alignment incorrectly classified 13% of the artificial chimeras versus 14% for CHECK_CHIMERA. Interestingly, only 1% of nonchimeras and 10% of chimeras were misclassified by both programs, suggesting that optimum performance is obtained by using the two methods to assign sequences to three classes: high-probability nonchimeras, high-probability chimeras, and sequences that need further study by other means. This study suggests that k-tuple-based matching methods are more sensitive than alignment-based methods when there is significant parental sequence similarity, while the opposite becomes true as the sequences become more distantly related. The software and a World Wide Web-based server are available at http://www-hto.usc.edu/software/mglobal CHI.

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Selected References

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  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Amann R., Springer N., Ludwig W., Görtz H. D., Schleifer K. H. Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature. 1991 May 9;351(6322):161–164. doi: 10.1038/351161a0. [DOI] [PubMed] [Google Scholar]
  3. Barns S. M., Fundyga R. E., Jeffries M. W., Pace N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1609–1613. doi: 10.1073/pnas.91.5.1609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Choi B. K., Paster B. J., Dewhirst F. E., Göbel U. B. Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis. Infect Immun. 1994 May;62(5):1889–1895. doi: 10.1128/iai.62.5.1889-1895.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fox G. E., Stackebrandt E., Hespell R. B., Gibson J., Maniloff J., Dyer T. A., Wolfe R. S., Balch W. E., Tanner R. S., Magrum L. J. The phylogeny of prokaryotes. Science. 1980 Jul 25;209(4455):457–463. doi: 10.1126/science.6771870. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. 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]
  8. Kopczynski E. D., Bateson M. M., Ward D. M. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol. 1994 Feb;60(2):746–748. doi: 10.1128/aem.60.2.746-748.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  11. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Robison-Cox J. F., Bateson M. M., Ward D. M. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl Environ Microbiol. 1995 Apr;61(4):1240–1245. doi: 10.1128/aem.61.4.1240-1245.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. doi: 10.1016/0022-2836(81)90087-5. [DOI] [PubMed] [Google Scholar]
  14. Vingron M., Waterman M. S. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol. 1994 Jan 7;235(1):1–12. doi: 10.1016/s0022-2836(05)80006-3. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Waterman M. S., Eggert M., Lander E. Parametric sequence comparisons. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):6090–6093. doi: 10.1073/pnas.89.13.6090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Weller R., Ward D. M. Selective Recovery of 16S rRNA Sequences from Natural Microbial Communities in the Form of cDNA. Appl Environ Microbiol. 1989 Jul;55(7):1818–1822. doi: 10.1128/aem.55.7.1818-1822.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]

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