Microbiota in the apical root canal system of tooth with apical periodontitis

Abstract

Background Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral. Methods Four groups of specimens are considered, the apical part of root from diseased teeth with and without root canal treatment, and wisdom teeth extracted to avoid being impacted (tooth healthy control), as well as an additional healthy oral control from biofilm of the buccal mucosa. DNA was extracted from these specimens and the microbiome was examined through focusing on the V3-V4 hypervariable region of the 16S rRNA gene using sequencing on Illumina MiSeq platform. Composition and diversity of the bacterial community were tested for individual samples, and between-group comparisons were done through differential analysis to identify the significant changes. Results We observed reduced community richness and diversity in microbiota samples from diseased teeth compared to healthy controls. Through differential analysis between AP teeth and healthy teeth, we identified 49 OTUs significantly down-regulated as well as 40 up-regulated OTUs for AP. Conclusion This study provides a global view of the microbial community of the AP associated cohorts, and revealed that AP involved not only bacteria accumulated with a high abundance, but also those significantly reduced ones due to microbial infection. Electronic supplementary material The online version of this article (10.1186/s12864-019-5474-y) contains supplementary material, which is available to authorized users.

A Systematic Review of the Root Canal Microbiota Associated with Apical Periodontitis: Lessons from Next‐Generation Sequencing

“…In these cases, the teeth investigated were to be retained in the oral cavity. Seven studies (7/18) employed an ex vivo sampling methodology, in which the roots were extracted prior to sampling the microbiota . Six of these studies relied on cryo‐pulverization of root sections, a technique used in sectioning the apical extremity of the root, that is then ground at liquid nitrogen temperatures in dedicated freezer mills .…”

“…In addition to NECs, negative controls serve to assess the contamination background specific to the sampling site . Herein, 12 of 18 studies have included negative controls mainly taken from endodontic access cavities or external root surfaces after disinfection, to verify the relative “sterility” of the site prior to sampling . Among these 12 studies, four used vital teeth as negative controls, which could also be regarded as biological/healthy controls .…”

“…Herein, 12 of 18 studies have included negative controls mainly taken from endodontic access cavities or external root surfaces after disinfection, to verify the relative “sterility” of the site prior to sampling . Among these 12 studies, four used vital teeth as negative controls, which could also be regarded as biological/healthy controls . However, ten of 12 studies have assessed their negative controls solely by means of culture or PCR, whereas only two of 12 studies have actually sequenced their negative controls …”

“…Among these 12 studies, four used vital teeth as negative controls, which could also be regarded as biological/healthy controls . However, ten of 12 studies have assessed their negative controls solely by means of culture or PCR, whereas only two of 12 studies have actually sequenced their negative controls …”

“…Qian et al. were assessed with a “high risk” of bias because they reported the presence of a “highly abundant microbiota” in vital healthy dental pulps that they used as controls . A vital pulp, however, is a mesenchymal tissue physiologically devoid of microbiota where any bacterial presence is considered invasive and can only be transient in a healthy pulp .…”