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dc.contributor.authorZiesemer, Kirsten A
dc.contributor.authorMann, Allison E
dc.contributor.authorSankaranarayanan, Krithivasan
dc.contributor.authorSchroeder, Hannes
dc.contributor.authorOzga, Andrew T
dc.contributor.authorBrandt, Bernd W
dc.contributor.authorZaura, Egija
dc.contributor.authorWaters-Rist, Andrea
dc.contributor.authorHoogland, Menno
dc.contributor.authorSalazar-García, Domingo C
dc.contributor.authorAldenderfer, Mark
dc.contributor.authorSpeller, Camilla
dc.contributor.authorHendy, Jessica
dc.contributor.authorWeston, Darlene A
dc.contributor.authorMacDonald, Sandy J
dc.contributor.authorThomas, Gavin H
dc.contributor.authorCollins, Matthew J
dc.contributor.authorLewis, Cecil M
dc.contributor.authorHofman, Corinne
dc.contributor.authorWarinner, Christina
dc.date.accessioned2018-11-23T00:33:19Z
dc.date.available2018-11-23T00:33:19Z
dc.date.issued2015-11-13
dc.identifier.issn2045-2322
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/285854
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.
dc.format.mediumElectronic
dc.languageeng
dc.publisherSpringer Science and Business Media LLC
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectDental Calculus
dc.subjectHumans
dc.subjectBacteria
dc.subjectMethanobrevibacter
dc.subjectRNA, Ribosomal, 16S
dc.subjectPhylogeny
dc.subjectGene Amplification
dc.subjectNucleic Acid Conformation
dc.subjectArchaeology
dc.subjectFemale
dc.subjectMale
dc.subjectMetagenome
dc.subjectMetagenomics
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectMicrobiota
dc.subjectGastrointestinal Microbiome
dc.titleIntrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.
dc.typeArticle
prism.publicationDate2015
prism.publicationNameSci Rep
prism.startingPage16498
prism.volume5
dc.identifier.doi10.17863/CAM.33198
dcterms.dateAccepted2015-10-14
rioxxterms.versionofrecord10.1038/srep16498
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2015-11-13
dc.contributor.orcidCollins, Matthew [0000-0003-4226-5501]
dc.identifier.eissn2045-2322
rioxxterms.typeJournal Article/Review
cam.issuedOnline2015-11-13


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International