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

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, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower and Nicola Segata ()
Additional contact information
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
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
Moreno Zolfo: Department CIBIO, University of Trento
Evguenia Kopylova: Department of Pediatrics, University of California San Diego
Edoardo Pasolli: Department CIBIO, University of Trento
Rob Knight: Department of Pediatrics, 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
Nicola Segata: Department CIBIO, University of Trento

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16366-7

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