Comparative analysis of MinION and MiSeq using 16S rRNA gene amplicon sequencing in human gut microbiome

The genetic classification of microbial populations at high taxonomic resolution is crucial for clinical diagnosis and treatment. The classification of complex bacterial communities in the human gut was examined in this study by utilizing amplicon sequencing of the 16S ribosomal RNA (rRNA) gene. The influence of different sequencing platforms and amplicon regions on this classification was investigated. Nineteen human fecal samples were analyzed using both Nanopore MinION and Illumina MiSeq platforms.The main objective of the analysis was to assess how effectively these platforms can characterize gut microbiota at the Amplicon Sequence Variant (ASV), genus, and species levels, taking into account various amplicon regions within the 16S rRNA gene. The findings reveal significant disparities between the two platforms. In particular, the MinION platform demonstrates higher values in terms of ASV and species richness, as well as diversity (both alpha and beta diversity) compared to the MiSeq platform. These variations are dependent on the specific targeted amplicon region of the 16S rRNA gene. However, despite these differences in richness and diversity, there is a notable level of consistency observed in detecting the presence of dominant microbial taxa across both platforms, although their relative abundances varied significantly. Notably, the study emphasizes that the choice of primers used for amplification exerts the most significant impact on the classification results at the genus level, surpassing the influence of the sequencing platform itself. This research provides valuable insights into the strengths and limitations of long-read and short-read sequencing in the context of classifying complex gut microbiota, particularly in clinical microbiology.