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.

Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer

“…Long reads help alignment-based assignment of taxonomy as well, because of their increasing taxonomical information content. In this study, under the MinION T4 condition, all the environmental samples showed better taxonomic resolution at the genus level than that under MiSeq, the same as previously reported 17 , 48 . Many papers have been published on software developments and shorter running times with MinION.…”

“…Nygaard et al . 48 analysed building-dust microbiomes using MinION and MiSeq and showed that, at the genus and species levels, MinION reported greater taxonomic resolution than MiSeq. Long reads help alignment-based assignment of taxonomy as well, because of their increasing taxonomical information content.…”

Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome

“…Nevertheless, the short amplicon lengths used in most studies might not be adequate to properly resolve the topology at the tips of the phylogeny. While this should have no effect on the identification of phylogenetic clades with distinct z-scores compared to outgroups, it might affect the identification of specific SVs and thus full-length 16S rRNA gene amplicons [66][67][68] might be used to construct phylogenetic trees with highly supported topologies near the tips.…”

The Bad and the Good—Microorganisms in Cultural Heritage Environments—An Update on Biodeterioration and Biotreatment Approaches

“…Most commonly used short-read based technologies (<300 bp) enable reliable biodiversity investigation on the genus level at the maximum, while third-generation sequencing technologies make it possible to analyze the data on species or even the strain level due to longer sequencing reads [ 44 ]. Recent researches show that many species-level assignments could be done only with long-read sequences, thus indicating the importance of improved resolution for accurate assessment of degradation/pathogenicity potential of environmental samples, usually observed for certain species or strains, but not always on the genera level [ 23 , 45 ].…”