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Accurate determination of microbial diversity from 454 pyrosequencing data

Nature Methods volume 6, pages 639–641 (2009)Cite this article

Abstract

We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.

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Figure 1: OTU number as a function of percentage sequence difference for 90 pyrosequenced 16S rRNA gene clones of known sequence.
Figure 2: Proportion of sequences assigned to the correct OTU as a function of percentage sequence difference for pyrosequenced 16S rRNA gene clones of known sequence.

References

  1. Margulies, M. et al. Nature 437, 376–380 (2005).

    CAS  Article  Google Scholar 

  2. Quinlan, A.R., Stewart, D.A., Stromberg, M.P. & Marth, G.T. Nat. Methods 5, 179–181 (2008).

    CAS  Article  Google Scholar 

  3. Vacic, V., Jin, H., Zhu, J.-K. & Lonardi, S. Pac. Symp. Biocomput. 13, 75–86 (2008).

    Google Scholar 

  4. Fraley, C. & Raftery, A.E. Comput. J. 41, 578–588 (1998).

    Article  Google Scholar 

  5. Schloss, P.D. & Handelsman, J. Appl. Environ. Microbiol. 71, 1501–1506 (2005).

    CAS  Article  Google Scholar 

  6. Huber, J.A. et al. Science 318, 97–100 (2007).

    CAS  Article  Google Scholar 

  7. Roesch, L.F. et al. ISME J. 1, 283–290 (2007).

    CAS  Article  Google Scholar 

  8. Sogin, M.L. et al. Proc. Natl. Acad. Sci. USA 103, 12115–12120 (2006).

    CAS  Article  Google Scholar 

  9. Quince, C., Curtis, T.P. & Sloan, W.T. ISME J. 2, 997–1006 (2008).

    CAS  Article  Google Scholar 

  10. Wang, G.C.Y. & Wang, Y. Microbiology 142, 1107–1114 (1996).

    CAS  Article  Google Scholar 

  11. Ashelford, K.E., Chuzhanova, N.A., Fry, J.C., Jones, A.J. & Weightman, A.J. Appl. Environ. Microbiol. 72, 5734–5741 (2006).

    CAS  Article  Google Scholar 

  12. Cole, J.R. et al. Nucleic Acids Res. 37, D141–D145 (2009).

    CAS  Article  Google Scholar 

  13. Liu, Z.Z., DeSantis, T.Z., Andersen, G.L. & Knight, R. Nucleic Acids Res. 36, 11 (2008).

    Article  Google Scholar 

  14. Lozupone, C. & Knight, R. Appl. Environ. Microbiol. 71, 8228–8235 (2005).

    CAS  Article  Google Scholar 

  15. Eriksson, N. et al. PLOS Comput. Biol. 4, 13 (2008).

    Article  Google Scholar 

  16. Needleman, S.B. & Wunsch, C.D. J. Mol. Biol. 48, 443–453 (1970).

    CAS  Article  Google Scholar 

  17. Katoh, K., Kuma, K., Toh, H. & Miyata, T. Nucleic Acids Res. 33, 511–518 (2005).

    CAS  Article  Google Scholar 

  18. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L. & Mark Welch, D. Genome Biol. 8, 9 (2007).

    Article  Google Scholar 

  19. Edgar, R.C. Nucleic Acids Res. 32, 1792–1797 (2004).

    CAS  Article  Google Scholar 

  20. Altschul, S.F. et al. Nucleic Acids Res. 25, 3389–3402 (1997).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank K. Ashelford (University of Liverpool) for the preliminary bioinformatics analysis of the sequencing data and for making the Mallard code publicly available, S. Huse (Marine Biological Laboratory, Woods Hole) for providing the quickdist algorithm and R. Knight for commenting on the manuscript. C.Q. is supported by a Lord Kelvin Glasgow University fellowship, W.T.S. by an Engineering and Physical Sciences Research Council Advanced Fellowship, R.J.D. by a Royal Society fellowship. The Natural Environment Research Council funded sequencing.

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Authors and Affiliations

  1. Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK

    Christopher Quince & William T Sloan

  2. Department of Biology, University of Bergen, Bergen, Norway

    Anders Lanzén

  3. School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK

    Thomas P Curtis, Russell J Davenport, Ian M Head & L Fiona Read

  4. School of Biological Sciences, University of Liverpool, Liverpool, UK

    Neil Hall

Authors
  1. Christopher Quince
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  2. Anders Lanzén
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  3. Thomas P Curtis
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  4. Russell J Davenport
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  5. Neil Hall
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  6. Ian M Head
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  7. L Fiona Read
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  8. William T Sloan
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Contributions

T.P.C., R.J.D., I.M.H., C.Q. and W.T.S. designed the study. C.Q. devised algorithms and wrote software. A.L. and C.Q. performed analysis. R.J.D. and L.F.R. performed experiments. N.H. oversaw sequencing. T.P.C., R.J.D., N.H., I.M.H., A.L., C.Q., L.F.R. and W.T.S. wrote the paper.

Corresponding author

Correspondence to Christopher Quince.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1 and Supplementary Tables 1–3 (PDF 72 kb)

Supplementary Software

Archive containing Readme file and source code. (ZIP 303 kb)

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Quince, C., Lanzén, A., Curtis, T. et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6, 639–641 (2009). https://doi.org/10.1038/nmeth.1361

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