16S marine amplicon - Oxford Nanopore versus Ion Torrent. Comparing Nanopore MinION and Ion torrent sequencing of the 16S rRNA gene for marine samples using different pipelines and databases

Describing ocean microbiome community dynamics is important for understanding the metabolic, physiological and ecological roles of these microorganisms. Yet, the results of these analyses are strongly influenced by the methods used to obtain them. This study compared 16S amplicons sequenced using two different technologies, the Oxford Nanopore MinION and the Ion torrent S5 PGM. In addition, results from two pipelines (QIIME2 and MOTHUR) and two databases (SILVA and RDP) for the downstream taxonomic assignments were compared. The comparisons were applied to subsets of samples collected at three different locations in the Southern Benguela upwelling region: the nearshore area of an upwelling site, the surf-zone of a large bay, and a shelf sample just outside an upwelling cell. The Oxford Nanopore MinION is one of the newer third-generation sequencing technologies available, and is significantly more affordable, more user friendly and results in much longer read lengths than its competitors. Results are promising for the Nanopore sequences. Overall, marine microbial community composition was comparable across platforms and pipelines; however, the relative abundances varied depending on the sequencing and bioinformatics methods used.