Comparison of the performance of MiSeq and NovaSeq in oral microbiome study

ABSTRACT

Objective

Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study.

Methods

Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens.

Results

NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades.

Conclusion

Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.

KEYWORDS:

• Oral microbiome
• MiSeq
• NovaSeq
• next generation sequencing
• Streptococcus

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The raw sequencing data have been deposited in NCBI GenBank under BioProject ID PRJEB73332.

Additional information

Funding

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education [NRF-2017M3A9B6062021, NRF-2023R1A2C2002783]. This work was supported by a 2-Year Research Grant of Pusan Na-tional University.