MetaPhlAn2 for enhanced metagenomic taxonomic profiling (original) (raw)

Nature Methods volume 12, pages 902–903 (2015)Cite this article

Subjects

An Erratum to this article was published on 30 December 2015

This article has been updated

To the Editor:

MetaPhlAn (metagenomic phylogenetic analysis)1 is a method for characterizing the taxonomic profiles of whole-metagenome shotgun (WMS) samples that has been used successfully in large-scale microbial community studies2,3. This work complements the original species-level profiling method with a system for eukaryotic and viral quantitation, strain-level identification and strain tracking. These and other extensions make the MetaPhlAn2 computational package (http://segatalab.cibio.unitn.it/tools/metaphlan2/ and Supplementary Software) an efficient tool for mining WMS samples.

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

Relevant articles

Open Access articles citing this article.

Access options

Subscribe to this journal

Receive 12 print issues and online access

$259.00 per year

only $21.58 per issue

Buy this article

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

Additional access options:

Figure 1: MetaPhlAn2 can accurately reconstruct the taxonomic composition of shotgun metagenomes.

Change history

In the version of this article initially published, MetaPhlAn was mislabeled as MetaphlAn2 in the key to Figure 1a (blue stars). The error has been corrected in the HTML and PDF versions of the article.

References

  1. Segata, N. et al. Nat. Methods 9, 811–814 (2012).
    Article CAS Google Scholar
  2. The Human Microbiome Project Consortium. Nature 486, 207–214 (2012).
  3. Scher, J.U. et al. Elife 2, e01202 (2013).
    Article Google Scholar
  4. Sunagawa, S. et al. Nat. Methods 10, 1196–1199 (2013).
    Article CAS Google Scholar
  5. Wood, D.E. & Salzberg, S. Genome Biol. 15, R46 (2014).
    Article Google Scholar
  6. Grice, E.A. et al. Science 324, 1190–1192 (2009).
    Article CAS Google Scholar

Download references

Acknowledgements

We thank S. Farina and M. Cristofolini for skin-sample collection, V. De Sanctis and R. Bertorelli for metagenomic sequencing, B. Ren for help in the generation of the synthetic metagenomes, the Human Microbiome Project Consortium, and the individuals from the Saint Louis, MO, and Houston, TX, areas, whose generous participation made the HMP possible. This work was supported in part by the US National Institutes of Health (grants R01HG005969 and U54DE023798 to C.H.), the US National Science Foundation (grant DBI-1053486 to C.H.), the US Army Research Office (grant W911NF-11-1-0473 to C.H.), Danone Research (grant PLF-5972-GD to G.W.) the European Union Seventh Framework Programme (Marie Curie grant PCIG13-618833 to N.S.), the Italian Ministry of Education, University and Research (grant FIR RBFR13EWWI to N.S.), Fondazione Caritro (grant Rif.Int.2013.0239 to N.S.) and Terme di Comano (grant to N.S.).

Author information

Authors and Affiliations

  1. Centre for Integrative Biology, University of Trento, Trento, Italy
    Duy Tin Truong, Matthias Scholz, Edoardo Pasolli, Adrian Tett & Nicola Segata
  2. Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts, USA
    Eric A Franzosa, Timothy L Tickle, George Weingart & Curtis Huttenhower
  3. The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Eric A Franzosa, Timothy L Tickle & Curtis Huttenhower

Authors

  1. Duy Tin Truong
    You can also search for this author inPubMed Google Scholar
  2. Eric A Franzosa
    You can also search for this author inPubMed Google Scholar
  3. Timothy L Tickle
    You can also search for this author inPubMed Google Scholar
  4. Matthias Scholz
    You can also search for this author inPubMed Google Scholar
  5. George Weingart
    You can also search for this author inPubMed Google Scholar
  6. Edoardo Pasolli
    You can also search for this author inPubMed Google Scholar
  7. Adrian Tett
    You can also search for this author inPubMed Google Scholar
  8. Curtis Huttenhower
    You can also search for this author inPubMed Google Scholar
  9. Nicola Segata
    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toNicola Segata.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

About this article

Cite this article

Truong, D., Franzosa, E., Tickle, T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling.Nat Methods 12, 902–903 (2015). https://doi.org/10.1038/nmeth.3589

Download citation

This article is cited by