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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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

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

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Peer Bork.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8, and Supplementary Tables 4, 5 and 7

Excel files

  1. 1.

    Supplementary Table 1

    Prokaryotic reference genomes used in this study.

  2. 2.

    Supplementary Table 2

    Summary of benchmark results for speed and accuracy of marker gene identification.

  3. 3.

    Supplementary Table 3

    Metagenomic data sets used in this study.

  4. 4.

    Supplementary Table 6

    Summary of mOTU linkage groups with taxonomic annotations.

Zip files

  1. 1.

    Supplementary Software

    mOTU profiling tool.

About this article

Publication history

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DOI

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

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