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dc.contributor.authorRaju, Sajan C.
dc.contributor.authorLagström, Sonja
dc.contributor.authorEllonen, Pekka
dc.contributor.authorde Vos, Willem M.
dc.contributor.authorEriksson, Johan Gunnar
dc.contributor.authorWeiderpass, Elisabete
dc.contributor.authorRounge, Trine Ballestad
dc.date.accessioned2019-05-14T12:01:08Z
dc.date.available2019-05-14T12:01:08Z
dc.date.issued2018-03-18
dc.description.abstractCulture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.en_US
dc.description.sponsorshipFolkhälsan Research Foundation; Academy of Finland Life and Health Medical Fund The Swedish Cultural Foundation in Finland Signe and Ane Gyllenberg Foundation Yrjö Jahnsson Foundationen_US
dc.descriptionSource at <a href=https://doi.org/10.1016/j.mimet.2018.03.003>https://doi.org/10.1016/j.mimet.2018.03.003. </a>en_US
dc.identifier.citationRaju, S.C., Lagström, S, Ellonen, P., de Vos, W.M., Eriksson, J.G., Weiderpass, E. & Rounge, T.B. (2018). Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling. <i>Journal of Microbiological Methods, 147</i>, 76-86. https://doi.org/10.1016/j.mimet.2018.03.003en_US
dc.identifier.cristinIDFRIDAID 1592878
dc.identifier.doi10.1016/j.mimet.2018.03.003
dc.identifier.issn0167-7012
dc.identifier.issn1872-8359
dc.identifier.urihttps://hdl.handle.net/10037/15301
dc.language.isoengen_US
dc.publisherElsevieren_US
dc.relation.journalJournal of Microbiological Methods
dc.rights.accessRightsopenAccessen_US
dc.subjectVDP::Medical disciplines: 700::Health sciences: 800::Community medicine, Social medicine: 801en_US
dc.subjectVDP::Medisinske Fag: 700::Helsefag: 800::Samfunnsmedisin, sosialmedisin: 801en_US
dc.titleReproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profilingen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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