A1 Refereed original research article in a scientific journal
Greengenes2 unifies microbial data in a single reference tree
Authors: McDonald, Daniel; Jiang, Yueyu; Balaban, Metin; Cantrell, Kalen; Zhu, Qiyun; Gonzalez, Antonio; Morton, James T.; Nicolaou, Giorgia; Parks, Donovan H.; Karst, Søren M.; Albertsen, Mads; Hugenholtz, Philip; DeSantis, Todd; Song, Se Jin; Bartko, Andrew; Havulinna, Aki S.; Jousilahti, Pekka; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Lahti, Leo; Mirarab, Siavash; Knight, Rob
Publisher: NATURE PORTFOLIO
Publication year: 2024
Journal: Nature Biotechnology
Journal acronym: NAT BIOTECHNOL
Volume: 42
First page : 715
Last page: 718
Number of pages: 10
ISSN: 1087-0156
eISSN: 1546-1696
DOI: https://doi.org/10.1038/s41587-023-01845-1
Publication's open availability at the time of reporting: Open Access
Publication channel's open availability : Partially Open Access publication channel
Web address : https://doi.org/10.1038/s41587-023-01845-1
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/180751073
Self-archived copy's licence: CC BY
Self-archived copy's version: Publisher`s PDF
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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