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 Niiranen

Mohit Jain, Veikko Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight

Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

540 Scopus citations

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 (US)
Pages (from-to)	715-718
Number of pages	4
Journal	Nature Biotechnology
Volume	42
Issue number	5
DOIs	https://doi.org/10.1038/s41587-023-01845-1
State	Published - May 2024

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Biomedical Engineering
Molecular Medicine

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10.1038/s41587-023-01845-1

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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(5), 715-718. https://doi.org/10.1038/s41587-023-01845-1

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, no. 5, pp. 715-718. https://doi.org/10.1038/s41587-023-01845-1

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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.",

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",

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

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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

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Greengenes2 unifies microbial data in a single reference tree

Abstract

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