Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection

Recently, the human gut microbiota has been implicated in various diseases such as immunological and neuropsychiatric disorders, and comprehensive gut microbiota analysis by metagenomic analysis using next-generation sequencers has been attracting attention. In this study, we compared microbial communities of 16S rDNA metagenome sequencing (16S-meta) and whole genome metagenome sequencing (WG-meta) using the nanopore sequencer MinION and 16S-meta using the Illumina Miseq sequencer with simulated and fecal samples, and evaluated the ability of WG-meta to detect antimicrobial resistance genes. We used the commercial Microbial Community DNA Standard as the DNA standard and a simulated sample comprising 17 strains of 15 bacterial species. In the detection of antimicrobial resistance genes, we used a simulated sample and spiked fecal samples containing Escherichia coli carrying blaCTX-M-27, Klebsiella pneumoniae carrying blaOXA-48, and Staphylococcus aureus carrying mecA. WG-meta using MinION was superior to 16S-meta and could accurately analyze the microbial communities at the species level, but it underestimated or misidentified the Bacillus subtilis group, Cryptococcus neoformans, Shigella sonnei, and Campylobacter jejuni. WG-meta using MinION could analyze the microbial communities in 5 min, and antimicrobial resistance gene detection using WG-meta could be performed in >30 min in the simulated sample with fewer bacterial counts. •Whole genome metagenome sequencing is superior to 16S rDNA metagenome sequencing.•Nanopore sequencer can identify diversity in a very short time.•Nanopore sequencer can detect antimicrobial-resistant gene in 30 min or more.