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Greengenes2 unifies microbial data in a single reference tree.
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.
Afiliación
  • McDonald D; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
  • Jiang Y; Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
  • Balaban M; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
  • Cantrell K; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
  • Zhu Q; School of Life Sciences, Arizona State University, Tempe, AZ, USA.
  • Gonzalez A; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.
  • Morton JT; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
  • Nicolaou G; Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
  • Parks DH; Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
  • Karst SM; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
  • Albertsen M; Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA.
  • Hugenholtz P; Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
  • DeSantis T; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
  • Song SJ; Department of Informatics, Second Genome, Brisbane, CA, USA.
  • Bartko A; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
  • Havulinna AS; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
  • Jousilahti P; Finnish Institute for Health and Welfare, Helsinki, Finland.
  • Cheng S; Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland.
  • Inouye M; Finnish Institute for Health and Welfare, Helsinki, Finland.
  • Niiranen T; Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
  • Jain M; Cedars-Sinai Medical Center, Los Angeles, CA, USA.
  • Salomaa V; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
  • Lahti L; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
  • Mirarab S; Finnish Institute for Health and Welfare, Helsinki, Finland.
  • Knight R; Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland.
Nat Biotechnol ; 2023 Jul 27.
Article en En | MEDLINE | ID: mdl-37500913
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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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Año: 2023 Tipo del documento: Article
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Año: 2023 Tipo del documento: Article