Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing

Area of Science:

• Microbiology
• Endodontics
• Genomics

Background:

• Chronic irreversible pulpitis is poorly understood at the microbial level.
• Current molecular methods are insufficient for characterizing the pulpal microbiome.
• Endodontic intervention is often necessary due to irreversible pulpitis.

Purpose of the Study:

• To comprehensively elucidate the microbiome in chronic irreversible pulpitis using shotgun metagenomic sequencing.
• To augment the understanding of pulpal pathogenesis.
• To identify novel microbial players in endodontic infections.

Main Methods:

• Shotgun metagenomic sequencing of pulpal tissue from six subjects (18-35 years) with chronic irreversible pulpitis.
• Aseptic sample procurement and DNA extraction using QIAamp DNA Mini Kit.
• Bioinformatic analysis with WGSA2 pipeline for taxonomic classification.

Main Results:

• Predominant phyla include Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%).
• Previously undocumented phyla such as Euryarchaeota, Thermoproteobacteria, Uroviricota, and Apicomplexa were identified.
• Propionibacterium acidifaciens was the most prevalent species; Streptococcus mutans was found in negligible amounts.
• Significant inter-subject variability in microbial diversity was observed.

Conclusions:

• Unprecedented microbial diversity in chronic irreversible pulpitis challenges existing endodontic paradigms.
• High taxonomic heterogeneity suggests standardized treatments may be inadequate.
• Identification of archaeal and viral components offers insights into persistent infections.
• Findings support evidence-based precision endodontics with patient-specific antimicrobial strategies.