Greengenes2 enables a shared data universe for microbiome studies

Daniel McDonald,Yueyu Jiang,Metin Balaban,Kalen Cantrell,Qiyun Zhu,Antonio Gonzalez,James T. Morton,Giorgia Nicolaou,Donovan H. Parks,Søren Karst,Mads Albertsen,Philip Hugenholtz,Todd DeSantis, Se Jin Song, Andrew Bartko, Aki S. Havulinna, Pekka Jousilahti, Susan Cheng, Mike Inouye, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Leo Lahti,Siavash Mirarab,Rob Knight

bioRxiv (Cold Spring Harbor Laboratory)(2023)

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摘要
16S rRNA and shotgun metagenomics studies typically yield different results, usually attributed to biases in PCR amplification of 16S rRNA genes. Here, we introduce Greengenes2 and show that differences in reference phylogeny are more important. 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 in phenotype effect size when analyzed with the same tree. ### Competing Interest Statement The authors have declared no competing interest.
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关键词
microbiome,data universe
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