Greengenes2 enables a shared data universe for microbiome studies

16S rRNA and shotgun metagenomics studies typically yield different results, traditionally thought to be due to biases in amplification. We 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.