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MetaPhlAn2 for enhanced metagenomic taxonomic profiling

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

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An Erratum to this article was published on 30 December 2015

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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.

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

Change history

  • 09 December 2015

    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.

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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.).

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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
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  2. Eric A Franzosa
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  3. Timothy L Tickle
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  4. Matthias Scholz
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  9. Nicola Segata
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Correspondence to Nicola Segata.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–22, Supplementary Table 1–13 and Supplementary Notes 1–7 (PDF 5854 kb)

Supplementary Software

Python-based MetaPhlAn2 software package (ZIP 37 kb)

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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

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