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Metagenomic species profiling using universal phylogenetic marker genes

Nature Methods volume 10, pages 1196–1199 (2013)Cite this article

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Abstract

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome–based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

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Figure 1: Phylogenetic marker gene–based mOTUs.
Figure 2: Phylogenetic analysis of mOTU linkage groups.
Figure 3: Performance and application of mOTU linkage groups.

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References

  1. Klappenbach, J.A., Saxman, P.R., Cole, J.R. & Schmidt, T.M. Nucleic Acids Res. 29, 181–184 (2001).

    Article  CAS  Google Scholar 

  2. Engelbrektson, A. et al. ISME J. 4, 642–647 (2010).

    Article  CAS  Google Scholar 

  3. Claesson, M.J. et al. Nucleic Acids Res. 38, e200 (2010).

    Article  Google Scholar 

  4. Gevers, D. et al. Nat. Rev. Microbiol. 3, 733–739 (2005).

    Article  CAS  Google Scholar 

  5. Arumugam, M. et al. Nature 473, 174–180 (2011).

    Article  CAS  Google Scholar 

  6. Liu, B., Gibbons, T., Ghodsi, M., Treangen, T. & Pop, M. BMC Genomics 12 (suppl. 2), S4 (2011).

  7. Segata, N. et al. Nat. Methods 9, 811–814 (2012).

    Article  CAS  Google Scholar 

  8. Ciccarelli, F. et al. Science 311, 1283–1287 (2006).

    Article  CAS  Google Scholar 

  9. Sorek, R. et al. Science 318, 1449–1452 (2007).

    Article  CAS  Google Scholar 

  10. von Mering, C. et al. Science 315, 1126–1130 (2007).

    Article  CAS  Google Scholar 

  11. Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P. Nat. Methods 10, 881–884 (2013).

    Article  CAS  Google Scholar 

  12. Qin, J. et al. Nature 464, 59–65 (2010).

    Article  CAS  Google Scholar 

  13. The Human Microbiome Project Consortium. Nature 486, 215–221 (2012).

  14. Nelson, K.E. et al. Science 328, 994–999 (2010).

    CAS  PubMed  Google Scholar 

  15. Walker, A.W. et al. ISME J. 5, 220–230 (2011).

    Article  CAS  Google Scholar 

  16. Mondot, S. et al. Inflamm. Bowel Dis. 17, 185–192 (2011).

    Article  CAS  Google Scholar 

  17. Schloissnig, S. et al. Nature 493, 45–50 (2013).

    Article  Google Scholar 

  18. Turnbaugh, P.J. et al. Nature 457, 480–484 (2009).

    Article  CAS  Google Scholar 

  19. Rajilic-Stojanovic, M., Heilig, H.G., Tims, S., Zoetendal, E.G. & de Vos, W.M. Environ. Microbiol. 15, 1146–1159 (2012).

    Article  Google Scholar 

  20. Manichanh, C., Borruel, N., Casellas, F. & Guarner, F. Nat. Rev. Gastroenterol. Hepatol. 9, 599–608 (2012).

    Article  CAS  Google Scholar 

  21. Rajilic-Stojanovic, M., Shanahan, F., Guarner, F. & de Vos, W.M. Inflamm. Bowel Dis. 19, 481–488 (2013).

    Article  Google Scholar 

  22. Png, C.W. et al. Am. J. Gastroenterol. 105, 2420–2428 (2010).

    Article  CAS  Google Scholar 

  23. Qin, J. et al. Nature 490, 55–60 (2012).

    Article  CAS  Google Scholar 

  24. Forslund, K. et al. Genome Res. 23, 1163–1169 (2013).

    Article  CAS  Google Scholar 

  25. Kultima, J.R. et al. PLoS ONE 7, e47656 (2012).

    Article  Google Scholar 

  26. Eddy, S.R. PLoS Comput. Biol. 7, e1002195 (2011).

    Article  CAS  Google Scholar 

  27. Muller, J., Creevey, C.J., Thompson, J.D., Arendt, D. & Bork, P. Bioinformatics 26, 263–265 (2010).

    Article  CAS  Google Scholar 

  28. Powell, S. et al. Nucleic Acids Res. 40, D284–D289 (2012).

    Article  CAS  Google Scholar 

  29. Mende, D.R. et al. PLoS ONE 7, e31386 (2012).

    Article  CAS  Google Scholar 

  30. Edgar, R.C. Bioinformatics 26, 2460–2461 (2010).

    Article  CAS  Google Scholar 

  31. Stamatakis, A. Bioinformatics 22, 2688–2690 (2006).

    Article  CAS  Google Scholar 

  32. Stamatakis, A. & Aberer, A. in Proceedings of the 2013 IEEE 27th International Symposium on Parallel and Distributed Processing 1195–1204 (2013).

  33. Berger, S.A. & Stamatakis, A. Bioinformatics 27, 2068–2075 (2011).

    Article  CAS  Google Scholar 

  34. Berger, S.A., Krompass, D. & Stamatakis, A. Syst. Biol. 60, 291–302 (2011).

    Article  Google Scholar 

  35. Letunic, I. & Bork, P. Bioinformatics 23, 127–128 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank members of the European Molecular Biology Laboratory Information Technologies core facility and Y. Yuan for managing the high-performance computing resources and the members of the Bork group for fruitful discussions. This work was supported by funding from European Molecular Biology Laboratory, the European Community's Seventh Framework Programme via the MetaHIT (HEALTH-F4-2007-201052) and International Human Microbiome Standards, (HEALTH-F4-2010-261376) grants, The Novo Nordisk Foundation, The Lundbeck Foundation, institutional funding by the Heidelberg Institute for Theoretical Studies and Deutsche Forschungsgemeinschaft grants STA 860/2 and STA 860/3, the Metagenopolis ANR-11-DPBS-0001 grant, and the European Research Council Advanced Grants (MicrobesInside and CancerBiome grant agreement numbers 250172 and 268985 to W.M.d.V. and P.B., respectively).

Author information

Authors and Affiliations

  1. European Molecular Biology Laboratory, Heidelberg, Germany

    Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap & Peer Bork

  2. The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany

    Fernando Izquierdo-Carrasco, Simon A Berger & Alexandros Stamatakis

  3. The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Manimozhiyan Arumugam, Oluf Pedersen & Jun Wang

  4. Beijing Genomics Institute (BGI) Shenzhen, Shenzhen, China

    Manimozhiyan Arumugam, Jun Wang & Junhua Li

  5. Unité de Service 1367 Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France

    Julien Tap, Joël Doré & S Dusko Ehrlich

  6. Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark

    Henrik Bjørn Nielsen, Simon Rasmussen & Søren Brunak

  7. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark

    Henrik Bjørn Nielsen & Søren Brunak

  8. Hagedorn Research Institute, Gentofte, Denmark

    Oluf Pedersen

  9. Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Oluf Pedersen

  10. Faculty of Health Sciences, Aarhus University, Aarhus, Denmark

    Oluf Pedersen

  11. Digestive System Research Unit, University Hospital Vall d'Hebron, Barcelona, Spain

    Francisco Guarner

  12. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands

    Willem M de Vos

  13. Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland

    Willem M de Vos

  14. King Abdulaziz University, Jeddah, Saudi Arabia

    Jun Wang

  15. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Jun Wang

  16. Macau University of Science and Technology, Macau, China

    Jun Wang

  17. BGI Hong Kong Research Institute, Hong Kong, China

    Junhua Li

  18. School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China

    Junhua Li

  19. Unité Mixte de Recherche 1319 Micalis, Institut National de la Recherche Agronomique, Jouy en Josas, France

    Joël Doré

  20. Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany

    Alexandros Stamatakis

  21. Max Delbrück Centre for Molecular Medicine, Berlin, Germany

    Peer Bork

Authors
  1. Shinichi Sunagawa
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  2. Daniel R Mende
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  3. Georg Zeller
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  4. Fernando Izquierdo-Carrasco
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  5. Simon A Berger
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  6. Jens Roat Kultima
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  7. Luis Pedro Coelho
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  8. Manimozhiyan Arumugam
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  9. Julien Tap
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  10. Henrik Bjørn Nielsen
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  11. Simon Rasmussen
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  12. Søren Brunak
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  13. Oluf Pedersen
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  14. Francisco Guarner
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  15. Willem M de Vos
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  16. Jun Wang
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  17. Junhua Li
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  18. Joël Doré
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  19. S Dusko Ehrlich
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  20. Alexandros Stamatakis
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  21. Peer Bork
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Contributions

P.B. and S.S. conceived the study, S.S., D.R.M., G.Z., F.I.-C., S.A.B., M.A., J.T. and A.S. designed and performed the analyses, S.S., D.R.M., G.Z., J.R.K., L.P.C. and J.L. developed and implemented the program, O.P., F.G., J.D. and J.W. provided data, S.S., D.R.M., G.Z. and P.B. wrote the manuscript, and M.A., J.T., H.B.N., S.R., O.P., F.G., W.M.d.V., S.D.E. and A.S. gave conceptual advice and revised the manuscript.

Corresponding author

Correspondence to Peer Bork.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, and Supplementary Tables 4, 5 and 7 (PDF 2053 kb)

Supplementary Table 1

Prokaryotic reference genomes used in this study. (XLSX 159 kb)

Supplementary Table 2

Summary of benchmark results for speed and accuracy of marker gene identification. (XLSX 13 kb)

Supplementary Table 3

Metagenomic data sets used in this study. (XLSX 21 kb)

Supplementary Table 6

Summary of mOTU linkage groups with taxonomic annotations. (XLSX 67 kb)

Supplementary Software

mOTU profiling tool. (ZIP 86115 kb)

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Cite this article

Sunagawa, S., Mende, D., Zeller, G. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 10, 1196–1199 (2013). https://doi.org/10.1038/nmeth.2693

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  • DOI: https://doi.org/10.1038/nmeth.2693

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