Fig. 1

16S rRNA gene sequence analysis using the MinION™ nanopore sequencer. a Workflow of 16S rRNA gene amplicon sequencing on the MinION™ platform. Sequencing libraries are generated by the four-primer PCR-based strategy, enabling simplified post-PCR adapter attachment. At the initial stage of PCR, the 16S rRNA gene is amplified with the inner primer pairs. The resulting PCR products are targeted for amplification with the outer primers to introduce the barcode and tag sequences at both ends, to which adapter molecules can be attached in a single-step reaction. b, c Taxonomic assignments of a mock community analyzed by MinION™ sequencing. The V1-V9 or V3-V4 region of the 16S rRNA gene was amplified from a pre-characterized mock community sample comprising ten bacterial species and sequenced on the MinION™ platform. Three thousand reads were randomly selected from the processed data set and aligned directly to the reference genome database of 5850 representative bacterial species. The pie charts represent taxonomic profiles at the (b) genus and (c) species levels. Even with the full-length 16S rRNA gene analysis, species-level resolution is not possible for Bacillus and Escherichia. Slices corresponding to misclassified (assigned to bacteria not present in the mock community) or unclassified (not classified at the given level but placed in a higher taxonomic rank) reads are exploded. The relative abundance (%) of each taxon is shown