Development of oral flora analysis methods useful for perioperative oral care

• Published in: Journal of Osaka Dental University Vol. 58; no. 1; pp. 295 - 303
• Main Authors: FUSHIZUKA, Hidekazu, MARUYAMA, Hugo, NAMBU, Takayuki, MASHIMO, Chiho, UCHIDA, Takuya, OKINAGA, Toshinori, MOMOTA, Yoshihiro
• Format: Journal Article
• Language: English
• Published: Osaka Odontological Society 25.04.2024
• Subjects: 16S rRNA; EPI2ME; Microbiome; NanoCLUST; Nanopore sequencing; Oral care
• ISSN: 0475-2058; 2189-6488
• DOI: 10.18905/jodu.58.1_295

The relationship between overall health and the oral flora has become clear with the development of oral flora analysis using next‐generation sequencing. Although Illumina (San Diego, CA, USA) sequencers are widely used for oral flora analysis, their short‐read nature poses some limitations, such as the inability to distinguish closely related bacterial species. Recently developed, the nanopore sequencer offers rapidly improving sequencing accuracy. The technology can read the full 16S rRNA gene, which has the potential to provide higher resolution in oral flora analysis. In this study, we utilized Illumina and nanopore sequencing methods to analyze saliva and interdental flora from two healthy adults and compared the outcomes of oral flora analysis. QIIME2 pipeline was used for Illumina sequence reads, while EPI2ME or NanoCLUST was utilized for nanopore reads. There was disagreement between Illumina and nanopore in the results of the oral flora analysis. Certain species exhibited a significant bias in detection through one of the sequencing methods, likely as a result of differences in the amplified region of 16S rRNA and the PCR primer utilized. Our findings suggest that utilizing the nanopore sequencer offers benefits when detecting certain species. Furthermore, optimizing the primers used during PCR could improve detection of species underrepresented in the nanopore. (J Osaka Dent Univ 2024; 58: 295-303)