Greengenes2 unifies microbial data in a single reference tree

2023/07/27 by Daniel McDonald, Yueyu Jiang, Metin Balaban +22 · 1 voice · 22 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Gut microbiota and health #Microbial Community Ecology and Physiology #Species Distribution and Climate Change

paper · pdf · doi:10.1038/s41587-023-01845-1

openalex publication_date 2023/07/27 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

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.

Citations

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Discussions

• Greengenes2 is a new reference tree integrating genomic and 16S rRNA databases, resolving discrepancies from PCR biases. It shows that 16S rRNA and shotgun metagenomics data from the same samples alig [bsky, 9 points, 0 comments]

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