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PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

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  • Nicola Segata

    (Harvard School of Public Health, 655 Huntington Avenue
    Present address: Centre for Integrative Biology, University of Trento, Via Sommarive 14, Trento 38123, Italy)

  • Daniela Börnigen

    (Harvard School of Public Health, 655 Huntington Avenue
    Broad Institute of Harvard and MIT, 301 Binney Street)

  • Xochitl C. Morgan

    (Harvard School of Public Health, 655 Huntington Avenue
    Broad Institute of Harvard and MIT, 301 Binney Street)

  • Curtis Huttenhower

    (Harvard School of Public Health, 655 Huntington Avenue
    Broad Institute of Harvard and MIT, 301 Binney Street)

Abstract

New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online.

Suggested Citation

  • Nicola Segata & Daniela Börnigen & Xochitl C. Morgan & Curtis Huttenhower, 2013. "PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes," Nature Communications, Nature, vol. 4(1), pages 1-11, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3304
    DOI: 10.1038/ncomms3304
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    Cited by:

    1. Hao Leng & Yinzhao Wang & Weishu Zhao & Stefan M. Sievert & Xiang Xiao, 2023. "Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Joanne S. Boden & Juntao Zhong & Rika E. Anderson & Eva E. Stüeken, 2024. "Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Li, Cun & Feng, Jing-Chun & Chen, Xiao & Zhou, Yingli & Liang, Jianzhen & Zhang, Si, 2024. "Behaviours of methane metabolism and community dynamics of methane anaerobic oxidation microbes on carbonate rocks with long-term cultivation in cold seep environment," Applied Energy, Elsevier, vol. 365(C).

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