Data released on January 14, 2016
The miniaturized and portable DNA sequencer MinION has been released to the scientific community in the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated a great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.
Using the R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. This data was sufficient for reconstruction of more than 90% of the 16S rRNA gene sequences for 20 different species present in a mock community used as a reference. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to make taxonomy assignments down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using "universal" primers.
Although nanopore-based sequencing produces reads with lower per-base accuracy in comparison with other platforms, the MinION DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements of the nanopore chemistry will further deliver more reliable information useful for the specific detection of microbial species and strains in complex ecosystems as a consequence of minimizing the basecalling errors and nucleotide bias as that reported here for 16S rRNA amplicon sequencing.