Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation

J Endod. 2015 Dec;41(12):1975-84. doi: 10.1016/j.joen.2015.08.022. Epub 2015 Oct 29.


Introduction: This study was conducted to evaluate the microbiomes of endodontic-periodontal lesions before and after chemomechanical preparation (CMP).

Methods: Clinical samples were taken from 15 root canals (RCs) with necrotic pulp tissues and from their associated periodontal pockets (PPs) (n = 15) of teeth with endodontic-periodontal lesions before and after CMP. The Human Oral Microbe Identification using Next Generation Sequencing (NGS) protocol and viable culture were used to analyze samples from RCs and PPs. The Mann-Whitney U test and Benjamini-Hochberg corrections were performed to correlate the clinical and radiographic findings with microbial findings (P < .05).

Results: Bacteria were detected in 100% of the samples in both sites (15/15) using NGS. Firmicutes was the most predominant phylum in both sites using both methods. The most frequently detected species in the RCs before and after CMP using NGS were Enterococcus faecalis, Parvimonas micra, Mogibacterium timidum, Filifactor alocis, and Fretibacterium fastidiosum. The species most frequently detected in the PPs before and after CMP using NGS were P. micra, E. faecalis, Streptococcus constellatus, Eubacterium brachy, Tannerella forsythia, and F. alocis. Associations were found between periapical lesions ≤ 2 mm and Desulfobulbus sp oral taxon 041 and with periodontal pockets ≥ 6 mm and Dialister invisius and Peptostreptococcus stomatis (all P < .05, found in the RCs before CMP).

Conclusions: It is concluded that the microbial community present in combined endodontic-periodontal lesions is complex and more diverse than previously reported. It is important to note that bacteria do survive in some root canals after CMP. Finally, the similarity between the microbiota of both sites, before and after CMP, suggests there may be a pathway of infection between the pulp and periodontium.

Keywords: Bacteria; Human Oral Microbe Identification using Next Generation Sequencing; culture; endodontic-periodontal lesions; next-generation sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Bacteria / isolation & purification
  • DNA, Bacterial / analysis
  • Dental Pulp Cavity / microbiology*
  • Dental Pulp Necrosis / microbiology*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Microbiota*
  • Middle Aged
  • Periapical Periodontitis / microbiology
  • Periodontal Pocket / microbiology*
  • Root Canal Preparation*


  • DNA, Bacterial