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

Life Sciences, School of (SOLS)

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

18 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)
Journal	Nature biotechnology
DOIs	https://doi.org/10.1038/s41587-023-01845-1
State	Accepted/In press - 2023

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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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. (Accepted/In press). Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology. 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 2023, 'Greengenes2 unifies microbial data in a single reference tree', Nature biotechnology. 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.",

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

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journal = "Nature biotechnology",

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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 - 2023

Y1 - 2023

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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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Greengenes2 unifies microbial data in a single reference tree

Abstract

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