Greengenes2 unifies microbial data in a single reference tree
: 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
: 2024
: Nature Biotechnology
: NAT BIOTECHNOL
: 42
: 715
: 718
: 10
: 1087-0156
: 1546-1696
DOI: https://doi.org/10.1038/s41587-023-01845-1
: https://doi.org/10.1038/s41587-023-01845-1
: https://research.utu.fi/converis/portal/detail/Publication/180751073
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.
