The apical root canal system microbial communities determined by next-generation sequencing

Abstract

The aim of this study was to explore the microbial communities of endodontic infections at their apical portion by 16S rRNA Illumina sequencing and delineate the core microbiome of root canal infections and that of their associated clinical symptomatology. Samples were collected from fifteen subjects presenting one tooth with a root canal infection, and their associated symptoms were recorded. Samples were collected from the apical third of roots using a #10 K file and then amplified using multiple displacement amplification and PCR-amplified with universal primers. Amplicons were sequenced (V3–V4 hypervariable region of the 16S rRNA gene) using MiSeq (Illumina, CA). The microbial composition of the samples was determined using QIIME and HOMINGS. Data were analyzed using t tests and ANOVA. A total of 1,038,656 good quality sequences were obtained, and OTUs were assigned to 10 bacterial phyla, led by Bacteroidetes (51.2%) and Firmicutes (27.1%), and 94 genera were represented primarily by Prevotella (17.9%) and Bacteroidaceae G-1 (14.3%). Symptomatic teeth were associated with higher levels of Porphyromonas (p < 0.05) and Prevotella. P. endodontalis and P. oris were present in both cores. The present study demonstrated the complexity of the root canal microbiome and the “common denominators” of root canal infections and identified taxa whose virulence properties should be further explored. The polymicrobial etiology of endodontic infections has long been established. However, few studies have focused on expanding the breadth and depth of coverage of microbiome-infected root canals at their apical portion.

A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

“…The oral cavity is an entry point to the human body, and microbial taxa colonizing the oral cavities can spread via epithelial surfaces to other body sites such as the stomach, intestinal tract, trachea, or lungs. In addition microbes are involved in diseases such as caries (oral decay) ( Gross et al, 2010 ; Tanner et al, 2018 ), periodontitis (gum disease) ( Joshipura et al, 2003 ; Schulz et al, 2019 ), endodontic infections (root canal) ( Brito et al, 2020 ), or tonsillitis ( Lemon et al, 2010 ; Galli et al, 2020 ), and have been increasingly linked to systemic diseases such as cardiovascular disease ( Beck and Offenbacher, 2005 ; Blekkenhorst et al, 2018 ), stroke ( Joshipura et al, 2003 ), diabetes ( Genco et al, 2005 ; Long et al, 2017 ), or pneumonia ( Seymour et al, 2007 ; Awano et al, 2008 ; Mammen et al, 2020 ). Recently it has become apparent that, rather than being caused by single organisms, many of these infections are linked to communities of organisms, often occurring in complex biofilms ( Hall-Stoodley et al, 2004 ; Jenkinson and Lamont, 2005 ; Bai et al, 2019 ).…”

Next-Generation Sequencing Analysis of Root Canal Microbiota Associated with a Severe Endodontic-Periodontal Lesion

“…Tooth and periodontal tissues can be affected by bacterial infectious diseases such as caries, pulpal and periapical pathologies and periodontitis [1,2].…”

Odontogenic Cervicofacial Necrotizing Fasciitis: Microbiological Characterization and Management of Four Clinical Cases

“…Aderhold et al already pointed out in 1981, and Eckert et al in 2000, the particular importance of the anaerobic species Prevotella, Porphyromonas, Fusobacterium and Peptostreptococcus [19,34]. Recent studies using molecular methods to determine the microbiome of odontogenic infections have confirmed these findings [14,16,17]. In addition to the previously mentioned bacteria, Parvimonas has also been associated with strong pathogenicity [18].…”

“…Sometimes, culture is not even able to detect any bacteria at all [7,8]. Using more recent molecular biological methods, it has been possible to detect a much larger number of bacteria in the root canals of non-vital teeth [14] and in odontogenic abscesses [15,16] than was previously possible using only cultural methods alone [17,18].…”