Intracanal microbiome profiles of two apical periodontitis cases in one patient: A comparison with saliva and plaque profiles

To determine the characteristics of the endodontic microbiome. Saliva, plaque, and infected root canal wall dentin of two teeth suffering from apical periodontitis were harvested from a 58-year-old man. Bacterial DNA was extracted from each sample, and 16S rRNA gene analysis targeting the V3-V4 region was conducted on the Illumina MiSeq platform using QIIME2. The functional potential of the microbiomes was inferred using PICRUSt2. The four microbiomes were different in structure and membership, yet the nine most abundant metabolic pathways were common among them. The two endodontic microbiomes were more anaerobic, rich in Firmicutes, and scarce in Actinobacteriota and Proteobacteria, compared with saliva and plaque microbiomes. Their profiles were dissimilar despite their clinical and radiographic similarities. The endodontic microbiomes were anaerobic, rich in Firmicutes, scarce in Actinobacteriota and Proteobacteria, and considerably varied within an individual.