Greengenes2 unifies microbial data in a single reference tree.

Journal

Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648

Informations de publication

Date de publication:
27 Jul 2023
Historique:
received: 16 12 2022
accepted: 25 05 2023
pubmed: 28 7 2023
medline: 28 7 2023
entrez: 27 7 2023
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1038/s41587-023-01845-1 PMID: 37500913
pubmed: 37500913
doi: 10.1038/s41587-023-01845-1
pii: 10.1038/s41587-023-01845-1
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NIA NIH HHS
ID : U19 AG063744
Pays : United States
Organisme : NIDDK NIH HHS
ID : U24 DK131617
Pays : United States

Commentaires et corrections

Type : ErratumIn

Informations de copyright

© 2023. The Author(s).

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Auteurs

Daniel McDonald (D)

Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.

Yueyu Jiang (Y)

Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.

Metin Balaban (M)

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.

Kalen Cantrell (K)

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Qiyun Zhu (Q)

School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
ORCID: 0000-0002-3568-6271

Antonio Gonzalez (A)

Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.

James T Morton (JT)

Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.

Giorgia Nicolaou (G)

Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA.

Donovan H Parks (DH)

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
ORCID: 0000-0001-6662-9010

Søren M Karst (SM)

Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA.

Mads Albertsen (M)

Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
ORCID: 0000-0002-6151-190X

Philip Hugenholtz (P)

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
ORCID: 0000-0001-5386-7925

Todd DeSantis (T)

Department of Informatics, Second Genome, Brisbane, CA, USA.

Se Jin Song (SJ)

Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.

Andrew Bartko (A)

Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-1237-2747

Aki S Havulinna (AS)

Finnish Institute for Health and Welfare, Helsinki, Finland.
Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland.
ORCID: 0000-0002-4787-8959

Pekka Jousilahti (P)

Finnish Institute for Health and Welfare, Helsinki, Finland.

Susan Cheng (S)

Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Michael Inouye (M)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

Teemu Niiranen (T)

Finnish Institute for Health and Welfare, Helsinki, Finland.
Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland.

Mohit Jain (M)

Sapient Bioanalytics, LLC, San Diego, CA, USA.

Veikko Salomaa (V)

Finnish Institute for Health and Welfare, Helsinki, Finland.
ORCID: 0000-0001-7563-5324

Leo Lahti (L)

Department of Computing, University of Turku, Turku, Finland.

Siavash Mirarab (S)

Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0001-5410-1518

Rob Knight (R)

Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA. robknight@eng.ucsd.edu.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. robknight@eng.ucsd.edu.
Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA. robknight@eng.ucsd.edu.
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. robknight@eng.ucsd.edu.
ORCID: 0000-0002-0975-9019

Classifications MeSH