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

View ORCID ProfileElin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
doi: https://doi.org/10.1101/193664
Elin Videvall
1Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, Lund 223 62, Sweden.
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  • ORCID record for Elin Videvall
Maria Strandh
1Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, Lund 223 62, Sweden.
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Anel Engelbrecht
2Directorate Animal Sciences, Western Cape Department of Agriculture, Private Bag X1, Elsenburg, South Africa.
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Schalk Cloete
2Directorate Animal Sciences, Western Cape Department of Agriculture, Private Bag X1, Elsenburg, South Africa.
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Charlie K. Cornwallis
1Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, Lund 223 62, Sweden.
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Abstract

The 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, 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 the direct PCR method for measuring host microbiomes has 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 MoBio PowerSoil DNA extraction kit in five distinct gut sample types (ileum – caecum – colon – faeces – 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 caecal, colon, and faecal samples. However, the two methods recovered significantly different microbiomes in 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 caecal, colon, and faecal 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 data, which will aid future gut microbiome studies of animals.

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Posted September 27, 2017.
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Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes
Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
bioRxiv 193664; doi: https://doi.org/10.1101/193664
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Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes
Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
bioRxiv 193664; doi: https://doi.org/10.1101/193664

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