Greengenes2 unifies microbial data in a single reference tree

Daniel McDonald; Yueyu Jiang; Metin Balaban; Kalen Cantrell; Qiyun Zhu; Antonio Gonzalez; James T. Morton; Giorgia Nicolaou; Donovan H. Parks; Søren M. Karst; Mads Albertsen; Philip Hugenholtz; Todd DeSantis; Se Jin Song; Andrew Bartko; Aki S. Havulinna; Pekka Jousilahti; Susan Cheng; Michael Inouye; Teemu Niiranen; Mohit Jain; Veikko Salomaa; Leo Lahti; Siavash Mirarab; Rob Knight

doi:10.1038/s41587-023-01845-1

Greengenes2 unifies microbial data in a single reference tree

Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T. Morton, Giorgia Nicolaou, Donovan H. Parks, Søren M. Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki S. Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu NiiranenMohit Jain, Veikko Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight^*

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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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.

Original language	English
Journal	Nature Biotechnology
Volume	42
Pages (from-to)	715–718
Number of pages	4
ISSN	1087-0156
DOIs	https://doi.org/10.1038/s41587-023-01845-1
Publication status	Published - May 2024

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10.1038/s41587-023-01845-1Licence: CC BY 4.0

Open Access ArticleFinal published version, 3.04 MBLicence: CC BY 4.0

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McDonald, D., Jiang, Y., Balaban, M., Cantrell, K., Zhu, Q., Gonzalez, A., Morton, J. T., Nicolaou, G., Parks, D. H., Karst, S. M., Albertsen, M., Hugenholtz, P., DeSantis, T., Song, S. J., Bartko, A., Havulinna, A. S., Jousilahti, P., Cheng, S., Inouye, M., ... Knight, R. (2024). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology, 42, 715–718. https://doi.org/10.1038/s41587-023-01845-1

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title = "Greengenes2 unifies microbial data in a single reference tree",

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.",

author = "Daniel McDonald and Yueyu Jiang and Metin Balaban and Kalen Cantrell and Qiyun Zhu and Antonio Gonzalez and Morton, {James T.} and Giorgia Nicolaou and Parks, {Donovan H.} and Karst, {S{\o}ren M.} and Mads Albertsen and Philip Hugenholtz and Todd DeSantis and Song, {Se Jin} and Andrew Bartko and Havulinna, {Aki S.} and Pekka Jousilahti and Susan Cheng and Michael Inouye and Teemu Niiranen and Mohit Jain and Veikko Salomaa and Leo Lahti and Siavash Mirarab and Rob Knight",

note = "{\textcopyright} 2023. The Author(s).",

year = "2024",

month = may,

doi = "10.1038/s41587-023-01845-1",

language = "English",

volume = "42",

pages = "715–718",

journal = "Nature Biotechnology",

issn = "1087-0156",

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McDonald, D, Jiang, Y, Balaban, M, Cantrell, K, Zhu, Q, Gonzalez, A, Morton, JT, Nicolaou, G, Parks, DH, Karst, SM, Albertsen, M, Hugenholtz, P, DeSantis, T, Song, SJ, Bartko, A, Havulinna, AS, Jousilahti, P, Cheng, S, Inouye, M, Niiranen, T, Jain, M, Salomaa, V, Lahti, L, Mirarab, S & Knight, R 2024, 'Greengenes2 unifies microbial data in a single reference tree', Nature Biotechnology, vol. 42, pp. 715–718. https://doi.org/10.1038/s41587-023-01845-1

TY - JOUR

T1 - Greengenes2 unifies microbial data in a single reference tree

AU - McDonald, Daniel

AU - Jiang, Yueyu

AU - Balaban, Metin

AU - Cantrell, Kalen

AU - Zhu, Qiyun

AU - Gonzalez, Antonio

AU - Morton, James T.

AU - Nicolaou, Giorgia

AU - Parks, Donovan H.

AU - Karst, Søren M.

AU - Albertsen, Mads

AU - Hugenholtz, Philip

AU - DeSantis, Todd

AU - Song, Se Jin

AU - Bartko, Andrew

AU - Havulinna, Aki S.

AU - Jousilahti, Pekka

AU - Cheng, Susan

AU - Inouye, Michael

AU - Niiranen, Teemu

AU - Jain, Mohit

AU - Salomaa, Veikko

AU - Lahti, Leo

AU - Mirarab, Siavash

AU - Knight, Rob

PY - 2024/5

Y1 - 2024/5

N2 - 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.

AB - 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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U2 - 10.1038/s41587-023-01845-1

DO - 10.1038/s41587-023-01845-1

M3 - Journal article

C2 - 37500913

AN - SCOPUS:85165868747

SN - 1087-0156

VL - 42

SP - 715

EP - 718

JO - Nature Biotechnology

JF - Nature Biotechnology

ER -

Greengenes2 unifies microbial data in a single reference tree

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Microflora Danica: The Microbiome of Denmark

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Greengenes2 unifies microbial data in a single reference tree

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Microflora Danica: The Microbiome of Denmark

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