A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

Abstract

There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques. Oxford Nanopore's MinION is the newest third generation sequencing technology on the market. With its many advantages such as portability, user friendliness, simplicity, speed of sequencing and long read length, the technology is now an actual contender to established sequencing platforms. MinION's main disadvantage is a relatively low read accuracy compared to several other platforms, although this is constantly improving. The present study, which appears to be the first of its kind, provides the results of a preliminary analysis of the microbial communities in indoor environments based on 16S rRNA gene amplicon sequencing, using both the Oxford Nanopore Technologies (ONT) MinIOn and the Illumina MiSeq DNA sequencers. At the level of family and above, there was no significant difference between the microbial compositions as revealed by the two platforms. However, at the genus, and particularly at the species level, the ONT MinION reported greater taxonomic resolution than Illumina MiSeq.

Figure 1

Heatmap of the 15 most abundant genera identified by mapping 16S rRNA gene amplicons sequenced on Illumina MiSeq and Nanopore MinION against the Greengenes reference database.

Figure 2

Heatmap of the 15 most abundant genera identified by mapping 16S rRNA gene amplicons sequenced on Illumina MiSeq and Nanopore MinION against the SILVA reference database.

Figure 3

Heatmap of the 15 most abundant species identified by mapping 16S rRNA gene amplicons sequenced on Illumina MiSeq and Nanopore MinION against the Greengenes reference database.

Figure 4

Heatmap of the 15 most abundant species identified by mapping 16S rRNA gene amplicons sequenced on Illumina MiSeq and Nanopore MinION against the SILVA reference database.

Figure 5

Correlation of identified taxa at (a) the genus level against GG, (b) genus level against SILVA, (c) species level against GG, and (d) species level against SILVA between sequencing platforms for all 12 samples. The dashed lines mark a 0.01% relative abundance threshold for each taxa for Nanopore and Illumina sequence data.