Comparative analysis of MinION and MiSeq using 16S rRNA Gene Amplicon sequencing in human gut microbiome

We conducted a comprehensive analysis of 19 human fecal samples using both the Nanopore MinION and the Illumina MiSeq platforms. We compared their performance in characterizing gut microbiota at the genus level focus on different amplicon regions of the 16S rRNA gene. Our findings revealed intriguing differences between the two platforms. Regarding species richness and diversity (alpha and beta diversity), the MinION platform exhibited comparatively higher values compared to the MiSeq platform, with variations depending on the specific targeted amplicon region of the 16S rRNA gene. Despite these differences in richness and diversity, we observed a high degree of consistence in detecting dominant high-abundance microbial species in both platforms. Notably, our study emphasized that the choice of primers used for amplification had the most significant impact on the classification results at the genus level, rather than the sequencing platform itself. Our research provides valuable insights into the strengths and limitations of long-read and short-read sequencing when it comes to classifying the complex gut microbiota in the field of clinical microbiology.