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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Author

Listed:
  • Francesco Asnicar

    (Department CIBIO, University of Trento)

  • Andrew Maltez Thomas

    (Department CIBIO, University of Trento)

  • Francesco Beghini

    (Department CIBIO, University of Trento)

  • Claudia Mengoni

    (Department CIBIO, University of Trento)

  • Serena Manara

    (Department CIBIO, University of Trento)

  • Paolo Manghi

    (Department CIBIO, University of Trento)

  • Qiyun Zhu

    (Department of Pediatrics, University of California San Diego)

  • Mattia Bolzan

    (Department CIBIO, University of Trento
    PreBiomics s.r.l)

  • Fabio Cumbo

    (Department CIBIO, University of Trento)

  • Uyen May

    (Department of Electrical and Computer Engineering, University of California San Diego)

  • Jon G. Sanders

    (Department of Pediatrics, University of California San Diego
    Cornell Institute for Host-Microbe Interaction and Disease, Cornell University)

  • Moreno Zolfo

    (Department CIBIO, University of Trento)

  • Evguenia Kopylova

    (Department of Pediatrics, University of California San Diego
    Clarity Genomics BVBA, Sint-Michielskaai 34, 2000)

  • Edoardo Pasolli

    (Department CIBIO, University of Trento
    University of Naples Federico II)

  • Rob Knight

    (Department of Pediatrics, University of California San Diego
    Department of Computer Science and Engineering, University of California San Diego
    Center for Microbiome Innovation, University of California San Diego
    Department of Bioengineering, University of California San Diego)

  • Siavash Mirarab

    (Department of Electrical and Computer Engineering, University of California San Diego)

  • Curtis Huttenhower

    (Department of Biostatistics, Harvard T. H. Chan School of Public Health
    The Broad Institute of MIT and Harvard)

  • Nicola Segata

    (Department CIBIO, University of Trento)

Abstract

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses.

Suggested Citation

  • Francesco Asnicar & Andrew Maltez Thomas & Francesco Beghini & Claudia Mengoni & Serena Manara & Paolo Manghi & Qiyun Zhu & Mattia Bolzan & Fabio Cumbo & Uyen May & Jon G. Sanders & Moreno Zolfo & Evg, 2020. "Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16366-7
    DOI: 10.1038/s41467-020-16366-7
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    Cited by:

    1. Shanlin Ke & Scott T. Weiss & Yang-Yu Liu, 2022. "Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Alice Risely & Arthur Newbury & Thibault Stalder & Benno I. Simmons & Eva M. Top & Angus Buckling & Dirk Sanders, 2024. "Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. Chrats Melkonian & Francisco Zorrilla & Inge Kjærbølling & Sonja Blasche & Daniel Machado & Mette Junge & Kim Ib Sørensen & Lene Tranberg Andersen & Kiran R. Patil & Ahmad A. Zeidan, 2023. "Microbial interactions shape cheese flavour formation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Sigal Leviatan & Saar Shoer & Daphna Rothschild & Maria Gorodetski & Eran Segal, 2022. "An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Guillermo Guerrero-Egido & Adrian Pintado & Kevin M. Bretscher & Luisa-Maria Arias-Giraldo & Joseph N. Paulson & Herman P. Spaink & Dennis Claessen & Cayo Ramos & Francisco M. Cazorla & Marnix H. Mede, 2024. "bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    7. Cameron Martino & Livia S. Zaramela & Bei Gao & Mallory Embree & Janna Tarasova & Seth J. Parker & Yanhan Wang & Huikuan Chu & Peng Chen & Kuei-Chuan Lee & Daniela Domingos Galzerani & Jivani M. Genga, 2022. "Acetate reprograms gut microbiota during alcohol consumption," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Haoyu Lang & Yuwen Liu & Huijuan Duan & Wenhao Zhang & Xiaosong Hu & Hao Zheng, 2023. "Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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