Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing

Abstract

Background: Apical periodontitis includes periapical granulomas and radicular cysts, which are histologically distinguished by the absence and the presence of an epithelial lining, respectively. The main cause of apical periodontitis is the bacterial colonization of the root canal space. This research aimed at assessing whether and how periapical granulomas and radicular cysts differ in terms of microbiota using high throughput amplicon target sequencing (HTS) techniques.

Methods: This study included 5 cases of Periapical Granulomas (PGs) and 5 cases of Radicular Cysts (RCs) selected on the base of histology out of 37 patients from January 2015 to February 2016. Complete medical history, panoramic radiograms (OPTs) and histologic records of each patient were assessed. Only lesions greater than 1 cm in diameter and developed in proximity to teeth with bad prognosis were included. The microbiota present in periapical granulomas and radicular cysts thus retrieved was finely characterized by pyrosequencing of the 16S rRNA genes.

Results: The core of OTUs shared between periapical granulomas and radicular cysts was dominated by the presence of facultative anaerobes taxa such as: Lactococcus lactis, Propionibacterium acnes, Staphylococcus warneri, Acinetobacter johnsonii and Gemellales. L. lactis, the main OTUs of the entire datasets, was associated with periapical granuloma samples. Consistently with literature, the anaerobic taxa detected were most abundant in radicular cyst samples. Indeed, a higher abundance of presumptive predicted metabolic pathways related to Lipopolysaccharide biosynthesis was found in radicular cyst samples.

Conclusions: The present pilot study confirmed the different microbial characterization of the two main apical periodontitis types and shade light on the possible role of L. lactis in periapical granulomas.

Keywords: Apical periodontitis (AP); High throughput amplicon target sequencing; Microbiota; Periapical granulomas (PGs); Radicular cysts (RCs).

Fig. 1

Abundance (%) of the major taxonomic groups detected by pyrosequencing. Only OTUs with an incidence above 0.2% are shown. Boxes represent the interquartile range (IQR) between the first and third quartiles, and the line inside represents the median (2nd quartile). Whiskers denote the lowest and the highest values within 1.56 IQR from the first and third quartiles, respectively. Circles represent outliers beyond the whiskers. Boxes are color coded according to the type Periapical Granulomas (PGs) blue and Radicular Cysts (RCs) red

Fig. 2

Principal Coordinate Analysis (PCoA) based on Weighted Unifrac distance matrix. Samples are color coded according of the type: Periapical Granulomas (PGs) red and Radicular Cysts (RCs) blue

Fig. 3

Significant co-occurrence and co-exclusion relationships between bacterial OTUs. Spearman’s rank correlation matrix of OTUs with > 0.2% abundance in at least 2 samples. The colors of the scale bar denote the nature of the correlation, with 1 indicating a perfectly positive correlation (dark blue) and − 1 indicating a perfectly negative correlation (dark red) between two microbial OTU. Only significant correlations (FDR < 0.05) are shown