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Updated: Jul 21, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Greengenes2 unifies microbial data in a single reference tree
Daniel McDonald1, Yueyu Jiang2, Metin Balaban3
1Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
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.
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