Comparison of Illumina versus Nanopore sequencing of the nasal microbiota.

Illumina and Nanopore 16S rRNA sequencing was performed on seventy nose swab samples collected from a population of children and adults. The MiSeq sequence data were processed using bioinformatics modules present in the mother v.1.36.1 software package. Local base calling in MinKNOW, workflows in EPI2ME and an in house developed bioinformatics script were used to analyze the Nanopore data. At genus level, similar bacterial diversity profiles were found and five main and established genera were identified by both platforms. However, the Nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, due to fixed default settings in the EPI2ME workflow, the bacterial genus Dolosigranulum was initially only identified at family level i.e. Carnobacteriaceae. Nanopore sequencing revealed a surprisingly wide range of different bacterial species.