Greengenes2 unifies microbial data in a single reference tree

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dc.contributor.authorMcDonald Daniel
dc.contributor.authorJiang Yueyu
dc.contributor.authorBalaban Metin
dc.contributor.authorCantrell Kalen
dc.contributor.authorZhu Qiyun
dc.contributor.authorGonzalez Antonio
dc.contributor.authorMorton James T.
dc.contributor.authorNicolaou Giorgia
dc.contributor.authorParks Donovan H.
dc.contributor.authorKarst Søren M.
dc.contributor.authorAlbertsen Mads
dc.contributor.authorHugenholtz Philip
dc.contributor.authorDeSantis Todd
dc.contributor.authorSong Se Jin
dc.contributor.authorBartko Andrew
dc.contributor.authorHavulinna Aki S.
dc.contributor.authorJousilahti Pekka
dc.contributor.authorCheng Susan
dc.contributor.authorInouye Michael
dc.contributor.authorNiiranen Teemu
dc.contributor.authorJain Mohit
dc.contributor.authorSalomaa Veikko
dc.contributor.authorLahti Leo
dc.contributor.authorMirarab Siavash
dc.contributor.authorKnight Rob
dc.contributor.organizationfi=data-analytiikka|en=Data-analytiikka|
dc.contributor.organizationfi=sisätautioppi|en=Internal Medicine|
dc.contributor.organizationfi=tyks, vsshp|en=tyks, varha|
dc.contributor.organization-code1.2.246.10.2458963.20.40502528769
dc.contributor.organization-code1.2.246.10.2458963.20.68940835793
dc.converis.publication-id180751073
dc.converis.urlhttps://research.utu.fi/converis/portal/Publication/180751073
dc.date.accessioned2025-08-27T20:48:33Z
dc.date.available2025-08-27T20:48:33Z
dc.description.abstract<p>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.</p>
dc.format.pagerange715
dc.format.pagerange718
dc.identifier.eissn1546-1696
dc.identifier.jour-issn1087-0156
dc.identifier.olddbid200271
dc.identifier.oldhandle10024/183298
dc.identifier.urihttps://www.utupub.fi/handle/11111/45978
dc.identifier.urlhttps://doi.org/10.1038/s41587-023-01845-1
dc.identifier.urnURN:NBN:fi-fe2025082784962
dc.language.isoen
dc.okm.affiliatedauthorNiiranen, Teemu
dc.okm.affiliatedauthorLahti, Leo
dc.okm.affiliatedauthorDataimport, tyks, vsshp
dc.okm.discipline3111 Biomedicineen_GB
dc.okm.discipline3111 Biolääketieteetfi_FI
dc.okm.internationalcopublicationinternational co-publication
dc.okm.internationalityInternational publication
dc.okm.typeA1 ScientificArticle
dc.publisherNATURE PORTFOLIO
dc.publisher.countryUnited Statesen_GB
dc.publisher.countryYhdysvallat (USA)fi_FI
dc.publisher.country-codeUS
dc.relation.doi10.1038/s41587-023-01845-1
dc.relation.ispartofjournalNature Biotechnology
dc.relation.volume42
dc.source.identifierhttps://www.utupub.fi/handle/10024/183298
dc.titleGreengenes2 unifies microbial data in a single reference tree
dc.year.issued2024

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