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

Roger Meisal,Hege S. Tunsjø,Anders B. Nygaard,Colin Charnock

doi:10.1038/s41598-020-59771-0

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.

Highlights

Built environments impact human health and disease, especially in countries where people spend a major part of the day indoors[1]
After quality filtering a total of 582032 sequence reads, with on average 48503 amplicon sequence variants (ASVs) per dust sample were kept for analysis (Table 1)
Sequencing of long-read 16S rRNA amplicons on Nanopore MinION generated a total of 2408076 sequence reads after basecalling, with on average 200673 sequence reads per sample

Summary

Introduction

Built environments impact human health and disease, especially in countries where people spend a major part of the day indoors[1]. Illumina sequencing platforms producing very high quality, but short (~ 300 bp) reads have been widely employed in the field of 16S rRNA amplicon sequencing[11]. This approach only permits analysis of a sub region of the 16S rRNA gene and taxonomic assignment of reads at the species level may be elusive. The major aim of the present study, restricted to a relatively small number of samples, was to investigate if the ONT MinION sequencing platform might offer promise for investigating the structure of the microbiota in dust collected from kindergartens and nursing homes. We consider how long-read sequences (ca. 1400 bp) obtained from the MinIon sequencer compare to short-read sequences (ca. 300 bp) obtained from Illumina MiSeq for classification of bacteria present in the indoor environment

Methods

Results

Discussion

Conclusion