TY - JOUR
T1 - Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
AU - Asnicar, Francesco
AU - Thomas, Andrew Maltez
AU - Beghini, Francesco
AU - Mengoni, Claudia
AU - Manara, Serena
AU - Manghi, Paolo
AU - Zhu, Qiyun
AU - Bolzan, Mattia
AU - Cumbo, Fabio
AU - May, Uyen
AU - Sanders, Jon G.
AU - Zolfo, Moreno
AU - Kopylova, Evguenia
AU - Pasolli, Edoardo
AU - Knight, Rob
AU - Mirarab, Siavash
AU - Huttenhower, Curtis
AU - Segata, Nicola
N1 - Funding Information:
This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 716575) to N.S. The work was also supported by MIUR “Futuro in Ricerca” RBFR13EWWI_001 and by the European Union (H2020-SFS-2018-1 project MASTER-818368 and H2020-SC1-BHC project ONCOBIOME-825410) to N.S. This study was also supported by the National Cancer Institute of the National Institutes of Health (1U01CA230551 to N.S.).
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-020-16366-7
DO - 10.1038/s41467-020-16366-7
M3 - Article
C2 - 32427907
AN - SCOPUS:85084964836
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 2500
ER -