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Accurate and universal delineation of prokaryotic species

Nature Methods volume 10, pages 881884 (2013) | Download Citation

Abstract

The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.

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Acknowledgements

We thank the members of the Bork group for helpful discussions and Y. Yuan and members of the European Molecular Biology Laboratory information technology core facility for managing the high-performance computing resources. We acknowledge funding provided by the CancerBiome project (European Research Council project reference 268985), the 'METACARDIS' project (FP7-HEALTH-2012-INNOVATION-I-305312) and the International Human Microbiome Standards project (HEALTH-F4-2010-261376).

Author information

Affiliations

  1. European Molecular Biology Laboratory, Heidelberg, Germany.

    • Daniel R Mende
    • , Shinichi Sunagawa
    • , Georg Zeller
    •  & Peer Bork
  2. Max Delbrück Centre for Molecular Medicine, Berlin, Germany.

    • Peer Bork

Authors

  1. Search for Daniel R Mende in:

  2. Search for Shinichi Sunagawa in:

  3. Search for Georg Zeller in:

  4. Search for Peer Bork in:

Contributions

P.B., D.R.M., S.S. and G.Z. designed the study. D.R.M. developed and implemented the program, D.R.M. and G.Z. performed the experiments, D.R.M., S.S. and G.Z. analyzed the data, and D.R.M., S.S., G.Z. and P.B. wrote 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, Supplementary Tables 1–3, 5–7, 15, 17, 19 and 20, and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 4

    NCBI Taxonomy information of type strains listed on the list of prokaryotic names with standing in nomenclature (LPSN;http://www.bacterio.net/) that could be linked to NCBI, including their sequencing status

  2. 2.

    Supplementary Table 8

    ANIb values of Prochlorococcusmarinus

  3. 3.

    Supplementary Table 9

    ANIm values of Prochlorococcusmarinus

  4. 4.

    Supplementary Table 10

    ANIb values of the Serratia and Rahnella clades

  5. 5.

    Supplementary Table 11

    ANIm values of the Serratia and Rahnella clades

  6. 6.

    Supplementary Table 12

    ANIb values of the Buchnera clade

  7. 7.

    Supplementary Table 13

    ANIm values of the Buchnera clade

  8. 8.

    Supplementary Table 14

    Cluster assignments for the 3,496 genomes used in this study

  9. 9.

    Supplementary Table 16

    Literature-based reclassifications of species assignments of NCBI Taxonomy database

  10. 10.

    Supplementary Table 18

    Assignments of genomes were previously not assigned to a named species to known species using the species clustering strategy presented in this publication

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DOI

https://doi.org/10.1038/nmeth.2575