Greengenes2 unifies microbial data in a single reference tree
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio González, James T. Morton, Giorgia Nicolaou, Donovan H. Parks, Søren Michael Karst, Mads Albertsen, Philip Hugenholtz, Todd Z. DeSantis, Se Jin Song, Andrew Bartko, Aki S. Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Abstract
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.