A 16S <scp>rRNA</scp> gene sequencing and analysis protocol for the Illumina MiniSeq platform

  • Monica Pichler
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • Ömer K. Coskun
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • Ana‐Sofia Ortega‐Arbulú
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • Nicola Conci
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • Gert Wörheide
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • Sergio Vargas
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
  • William D. Orsi
    Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany

この論文をさがす

説明

<jats:title>Abstract</jats:title><jats:p>High‐throughput sequencing of the 16S <jats:styled-content style="fixed-case">rRNA</jats:styled-content> gene on the Illumina platform is commonly used to assess microbial diversity in environmental samples. The MiniSeq, Illumina's latest benchtop sequencer, enables more cost‐efficient <jats:styled-content style="fixed-case">DNA</jats:styled-content> sequencing relative to larger Illumina sequencing platforms (<jats:italic>e.g.,</jats:italic> MiSeq). Here we used a modified custom primer sequencing approach to test the fidelity of the MiniSeq for high‐throughput sequencing of the V4 hypervariable region of 16S <jats:styled-content style="fixed-case">rRNA</jats:styled-content> genes from complex communities in environmental samples. To this end, we designed additional sequencing primers that enabled application of a dual‐index barcoding method on the MiniSeq. A mock community was sequenced alongside the environmental samples in four different sequencing runs as a quality control benchmark. We were able to recapture a realistic richness of the mock community in all sequencing runs, and identify meaningful differences in alpha and beta diversity in the environmental samples. Furthermore, rarefaction analysis indicated diversity in many environmental samples was close to saturation. These results show that the MiniSeq can produce similar quantities of high‐quality V4 reads compared to the MiSeq, yet is a cost‐effective option for any laboratory interested in performing high‐throughput 16S <jats:styled-content style="fixed-case">rRNA</jats:styled-content> gene sequencing.</jats:p>

収録刊行物

被引用文献 (2)*注記

もっと見る

問題の指摘

ページトップへ