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Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

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Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

dc.contributor.author	Ziesemer, Kirsten A.
dc.contributor.author	Mann, Allison E.
dc.contributor.author	Sankaranarayanan, Krithivasan
dc.contributor.author	Schroeder, Hannes
dc.contributor.author	Ozga, Andrew T.
dc.contributor.author	Brandt, Bernd W.
dc.contributor.author	Zaura, Egija
dc.contributor.author	Waters-Rist, Andrea
dc.contributor.author	Hoogland, Menno Lambertus Pieter
dc.contributor.author	Salazar García, Domingo Carlos
dc.contributor.author	Aldenderfer, Mark S.
dc.contributor.author	Speller, Camilla
dc.contributor.author	Hendy, Jessica
dc.contributor.author	Weston, Darlene A.
dc.contributor.author	MacDonald, Sandy J.
dc.contributor.author	Thomas, Gavin H.
dc.contributor.author	Collins, Matthew J.
dc.contributor.author	Lewis, Cecil M.
dc.contributor.author	Hofman, Corinne Lisette
dc.contributor.author	Warinner, Christina
dc.date.accessioned	2015-11-17T07:59:56Z
dc.date.available	2015-11-17T07:59:56Z
dc.date.issued	2015
dc.identifier.citation	Ziesemer, Kirsten A. Mann, Allison E. Sankaranarayanan, Krithivasan Schroeder, Hannes Ozga, Andrew T. Brandt, Bernd W. Zaura, Egija Waters-Rist, Andrea Hoogland, Menno Lambertus Pieter Salazar García, Domingo Carlos Aldenderfer, Mark S. Speller, Camilla Hendy, Jessica Weston, Darlene A. MacDonald, Sandy J. Thomas, Gavin H. Collins, Matthew J. Lewis, Cecil M. Hofman, Corinne Lisette Warinner, Christina 2015 Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification Scientific Reports 5 16498 1 19
dc.identifier.uri	http://hdl.handle.net/10550/48219
dc.description.abstract	To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341¿534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hyper variable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
dc.language.iso	eng
dc.relation.ispartof	Scientific Reports, 2015, vol. 5, num. 16498, p. 1-19
dc.subject	Prehistòria
dc.title	Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
dc.type	journal article	es_ES
dc.date.updated	2015-11-17T07:59:57Z
dc.identifier.doi	10.1038/srep16498
dc.identifier.idgrec	108119
dc.rights.accessRights	open access	es_ES