Abstract:Different high-throughput sequencing platforms have their own advantages and disadvantages. An appropriate sequencing platform for the research object is of great significance to the study of microbial diversity. Taking the bacteria in raw milk as the research object, Illumina MiSeq and IonS5 XL sequencing platforms were used to amplify and sequence the V4-V5 region of bacteria, and the applicability of two different sequencing platforms in the microbial diversity of raw milk was discussed. The results showed that all of the original sequencing data from the two platforms could meet the experimental requirements after quality control. The results of IonS5 XL sequencing on the number of annotated species at different taxonomic levels, alpha diversity, rarefaction curve, and rank abundance curve were superior to those of Illumina MiSeq sequencing, indicating higher community abundance in raw milk. The same dominant phyla and dominant genera were found in both Illumina MiSeq sequencing and IonS5 XL sequencing. The Venn plots and PCA analysis showed that Illumina MiSeq sequencing had better biological repeatability than IonS5 XL sequencing and had advantages in sequencing stability. If the statistics of parallel samples could be increased and the repeatability could be improved, IonS5 XL sequencing will have great application prospects in dairy microbial diversity research.
