Greengenes2 unifies microbial data in a single reference tree

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 p...

Full description

Saved in:
Bibliographic Details
Published in:Nature biotechnology Vol. 42; no. 5; pp. 715 - 718
Main Authors: McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, Knight, Rob
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01.05.2024
Nature Publishing Group
Subjects:
631/114/129
631/158/855
Agriculture
Bioinformatics
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Brief Communication
Communication
Computer engineering
Genomes
Genomics
Life Sciences
Metagenomics
Microorganisms
Phenotypes
Phylogenetics
Phylogeny
rRNA 16S
Taxonomy
ISSN:1087-0156, 1546-1696, 1546-1696
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. A comprehensive microbial resource reconciles genomic and 16S rRNA data in a single tree.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1087-0156
1546-1696
1546-1696
DOI:10.1038/s41587-023-01845-1