Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communication
  • Published:

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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).

    Article  CAS  Google Scholar 

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

    Article  CAS  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.

Author information

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anders Lanzén
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thomas P Curtis
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Russell J Davenport
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Neil Hall
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ian M Head
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. L Fiona Read
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. William T Sloan
    View author publications

    You can also search for this author in PubMed Google Scholar

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)

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1361

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing