Infected Dentin and Symptomatic Irreversible Pulpitis Share a Core Microbiome

INTRODUCTION: The objective of this clinical study was to identify and compare the bacterial taxa in teeth with infected dentin (ID) and its associated root canals with symptomatic irreversible pulpitis (SIP) using high-throughput next-generation sequencing. METHODS: Teeth diagnosed with symptomatic irreversible pulpitis were included, with samples collected from infected dentin adjacent to the pulp and from the root canal. A total of 20 samples were analyzed, comprising 10 from each site. The microbiomes were examined using 16S rRNA gene amplicon sequencing. RESULTS: At the phylum level, Firmicutes predominated in ID and SIP, followed by Proteobacteria, with all samples showing consistent detection of these phyla. Actinobacteria and Bacteroidetes were also frequently detected. At the genus level, both microbial communities were dominated by Lactobacillus, followed by Streptococcus and Olsenella. At the species level, however, the shared core microbiome was represented by individual taxa belonging to several predominant genera, including Lactobacillus ultunensis, Veillonella dispar, Streptococcus salivarius, Campylobacter rectus, Streptococcus parasanguinis clade 411, Oribacterium sp. HMT-078, and Fretibacterium fastidiosum. Notably, ID samples displayed a predominance of Gram-positive bacteria, accounting for 78.9% of the oral microbiota, whereas SIP samples showed a relative enrichment of Gram-negative anaerobes, which represented 31.5% of the community. CONCLUSION: In conclusion, ID and SIP samples shared a substantial core microbiome, supporting ecological continuity along the dentin-pulp infection pathway.