An easy-to-use nucleic acid-based fluidic platform for the profiling of oral microbiome from swab and mouthwash that consists of functionalized microbeads and a multi-chamber aliquoting structure

The oral microbiome is an important indicator of health status; however, it has the limitation of varying significantly over time and under different life conditions. Therefore, rapid and convenient analysis through automation is required. In this study, we developed an automated oral microbiome analysis platform for the rapid and convenient diagnosis of health using mouthwash as the sample. Functionalized microbeads coated with graphene oxide (GO) were employed to concentrate 5 mL of mouthwash sample into 300 μL within 3 min, achieving an eight-fold concentration. Effective adsorption of bacteria onto the functionalized microbeads was confirmed using scanning electron microscopy. Furthermore, nucleic acids were extracted from bacteria adsorbed on the functionalized microbeads via bead beating (3000 rpm) for 3 min, achieving approximately 100 % yield compared with conventional methods. The extracted nucleic acid solution was then automatically aliquoted into PCR 8-tube strips (2 μL each) with high accuracy (CV% = 2.63 %) using a simple fluidic aliquoting structure that incorporated an access channel and retention area. Oral microbiome profiling at the phylum level was compared between the developed fluidic cartridge method and commercial approaches, including next-generation sequencing (NGS) analysis. The automated platform, which integrates the developed sample pretreatment and aliquoting processes into a fluidic cartridge, successfully analyzed the oral health status of both humans and companion animals within 3 h, demonstrating analytical accuracy equivalent to that of NGS. • We developed an automated oral microbiome analysis platform using mouthwash for rapid and convenient health profiling. • The system integrates graphene oxide–coated microbeads for efficient sample concentration and nucleic acid extraction with a fluidic cartridge that precisely aliquots DNA for qPCR. • This platform provides oral microbiome profiling comparable to NGS and delivers accurate results within 3 h for both humans and companion animals.