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Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomes

dc.contributor.authorVidevall, Elinen_ZA
dc.contributor.authorStrandh, Mariaen_ZA
dc.contributor.authorEngelbrecht, Anelen_ZA
dc.contributor.authorCloete, Schalken_ZA
dc.contributor.authorCornwallis, Charlie K.en_ZA
dc.date.accessioned2018-08-07T07:03:50Z
dc.date.available2018-08-07T07:03:50Z
dc.date.issued2017
dc.identifier.citationVidevall, E. et al. 2017. Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomes. mSystems, 2(6):e00132-17, doi:10.1128/mSystems.00132-17.
dc.identifier.issn2379-5077 (online)
dc.identifier.otherdoi:10.1128/mSystems.00132-17
dc.identifier.urihttp://hdl.handle.net/10019.1/104234
dc.descriptionCITATION: Videvall, E. et al. 2017. Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomes. mSystems, 2(6):e00132-17, doi:10.1128/mSystems.00132-17.
dc.descriptionThe original publication is available at https://msystems.asm.org
dc.description.abstractThe gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies.en_ZA
dc.description.urihttps://msystems.asm.org/content/2/6/e00132-17
dc.format.extent13 pages
dc.language.isoen_ZAen_ZA
dc.publisherAmerican Society for Microbiology
dc.subjectPCRen_ZA
dc.titleDirect PCR offers a fast and reliable alternative to conventional DNA isolation methods for gut microbiomesen_ZA
dc.typeArticleen_ZA
dc.description.versionPublisher's version
dc.rights.holderAuthors retain copyright


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