Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
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Published:2023-02-23
Issue:11
Volume:41
Page:1633-1644
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ISSN:1087-0156
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Container-title:Nature Biotechnology
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language:en
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Short-container-title:Nat Biotechnol
Author:
Blanco-Míguez AitorORCID, Beghini FrancescoORCID, Cumbo FabioORCID, McIver Lauren J., Thompson Kelsey N.ORCID, Zolfo MorenoORCID, Manghi PaoloORCID, Dubois Leonard, Huang Kun D., Thomas Andrew Maltez, Nickols William A.ORCID, Piccinno GianmarcoORCID, Piperni ElisaORCID, Punčochář Michal, Valles-Colomer Mireia, Tett Adrian, Giordano Francesca, Davies RichardORCID, Wolf Jonathan, Berry Sarah E., Spector Tim D.ORCID, Franzosa Eric A.ORCID, Pasolli Edoardo, Asnicar FrancescoORCID, Huttenhower CurtisORCID, Segata NicolaORCID
Abstract
AbstractMetagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
Publisher
Springer Science and Business Media LLC
Subject
Biomedical Engineering,Molecular Medicine,Applied Microbiology and Biotechnology,Bioengineering,Biotechnology
Reference101 articles.
1. Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J. & Segata, N. Shotgun metagenomics, from sampling to analysis. Nat. Biotechnol. 35, 833–844 (2017). 2. Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012). 3. Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902–903 (2015). 4. Beghini, F. et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10, e65088 (2021). 5. Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104 (2017).
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