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Nature Methods
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Metagenomic species profiling using universal phylogenetic marker genes

Nature Methodsvolume 10, pages1196–1199 (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 athttp://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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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 toPeer 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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Sunagawa, S., Mende, D., Zeller, G.et al. Metagenomic species profiling using universal phylogenetic marker genes.Nat Methods10, 1196–1199 (2013). https://doi.org/10.1038/nmeth.2693

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