A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer

The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa. To assess capabilities, three fungal mock communities were sequenced, each of which had varying ratios of 16 taxa. The data were processed through our selected pipeline. The MinION recovered all mock community members, when mixed at equal ratios. When a taxon was represented at a lower ratio, it was not recovered or decreased in relative abundance. Despite high error rates, highly accurate consensus sequences can be derived. This methodological approach identified all mock community taxa, demonstrating the MinION can be used as a practical alternative to profile fungal communities.