Comparation of Illumina MiSeq and NovaSeq platforms in analysis of human gut and vaginal microbiota profiles

Illumina MiSeq and NovaSeq are commonly used platforms for 16S rRNA gene sequencing to resolve microbiota structure, but the similarities and differences between the two platforms for microbiota structure analysis remain unclear. In this research, the 16S rRNA gene V3-V4 regions of 10 human fecal samples and 8 human vaginal swab samples were amplified using PCR primers applicable to MiSeq and NovaSeq platforms respectively, the same PCR reaction system and reaction procedures, and sequenced on the respective platforms, and the data were processed using a unified bioinformatics process.