Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Open accessAbstract
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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StrainPhlAn 3 and PanPhlAn 3 can be combined with PhyloPhlAn 3 and HUMAnN 3 to provide multiple complementary culture-independent means to investigate strain-level diversity from new or public metagenomes.
“StrainPhlan 3 and PanPhlAn 3 can thus be combined with PhyloPhlAn 3 (Asnicar et al., 2020) and HUMAnN 3 to provide multiple, complementary, culture-independent means to investigate the strain-level diversity of taxa in the microbiome, from new data or by re-using thousands of publicly available metagenomes.”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Asnicar et al., 2020
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References 77 · Cited by 869
- Authors
- Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., Sanders, J. G., Zolfo, M., Kopylova, E., Pasolli, E., Knight, R., Mirarab, S., Huttenhower, C., & Segata, N.
- Affiliations
- University of Trento (IT)
- University of California San Diego (US)
- Cornell University (US)
- Broad Institute (US)
- Corresponding author
- Segata, Nicola
- ORCID
- Venue
- Nature Communications
- Published
- 2020-05-19
- Volume
- 11
- Issue
- 1
- Pages
- 2500-2500
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7237447
- OpenAlex
- W3028280407
- Cited by
- 869
- References
- 77
- Citations by year
- 2026: 162 · 2025: 166 · 2024: 175 · 2023: 128 · 2022: 138 · 2021: 87 · 2020: 11
- FWCI
- 33.01
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by-nd)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- European Commission (H2020 SC1, 716575, 825410, SC1-BHC, H2020-SFS-2018-1, HORIZON2020, 818368, H2020, H2020-SC1-BHC)
- Ministero dell’Istruzione, dell’Università e della Ricerca (H2020, RBFR13EWWI_001)
- National Institutes of Health (1u01ca230551-01a1, H2020, 1U01CA230551)
- Horizon 2020 Framework Programme (MASTER-818368, OncoBiome 825410, 818368, SC1-BHC, H2020-SC1, 825410)
- National Cancer Institute (1U01CA230551, U01 CA230551, R01CA230551)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- metagenome-assembled genomes, microbial genomes, gut metagenome, Staphylococcus aureus isolates, metagenomics
- MeSH terms
- Bacteria, Phylogeny, Genome, Bacterial, Metagenome, Metagenomics, Genome, Microbial
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