“…Usually, nanopore sequencing achieves a higher number of taxa at the species level than Illumina sequencing (2), most likely explained by the capacity of nanopore sequencing reads to span multiple 16S rRNA variable regions (2). Indeed, nanopore sequencing approaches rely on longer reads and reference databases are mostly composed of standard and shorter gene markers, such as fragments of the 16S rRNA gene or the ITS region (3,4). Therefore, nanopore sequencing may have limited reliability in profiling unknown microbial communities, decreasing the confidence on the taxonomical composition obtained (5).…”