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

dc.contributor.authorWarriner, Christina
dc.contributor.authorLewis, Cecil
dc.contributor.authorMann, Allison
dc.contributor.authorSankaranarayanan, Krithivasan
dc.contributor.authorOzga, Andrew
dc.date.accessioned2016-01-18T03:30:45Z
dc.date.accessioned2016-03-30T15:32:18Z
dc.date.available2016-01-18T03:30:45Z
dc.date.available2016-03-30T15:32:18Z
dc.date.issued2015-11-13
dc.description.abstractTo 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 hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.en_US
dc.description.peerreviewYesen_US
dc.identifier.doi10.1038/srep16498en_US
dc.identifier.urihttp://hdl.handle.net/11244/25616
dc.languageen_USen_US
dc.relation.ispartofseriesScientific Reports;16498
dc.subjectMicrobial geneticsen_US
dc.subjectEnvironmental microbiologyen_US
dc.subjectMicrobial ecologyen_US
dc.titleIntrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplificationen_US
dc.typeArticleen_US
ou.groupCollege of Arts and Sciences::Department of Anthropologyen_US

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