Table of Contents  
Year : 2022  |  Volume : 14  |  Issue : 1  |  Page : 52-61

Oral Microbes Associated with Pulp and Periapical Infections

1 Department of Oral and Maxillofacial Pathology, PMS College of Dental Science and Research, Thiruvananthapuram, Kerala, India
2 Department of Oral and Maxillofacial Pathology, Azeezia College of Dental Science and Research, Kollam, Kerala, India

Date of Submission27-Nov-2021
Date of Decision23-Apr-2022
Date of Acceptance25-Apr-2022
Date of Web Publication05-Aug-2022

Correspondence Address:
Dr. Bonnis Benny
Department of Oral and Maxillofacial Pathology, PMS College of Dental Science and Research, Golden Hills, Vattapara, Venkode, Thiruvananthapuram, Kerala 695028
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jofs.jofs_268_21

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Intoduction: Endodontic treatment procedures are designed to eradicate infection and prevent germs from infecting or reinfecting the root and/or periapical tissues. As a result, a thorough understanding of the endodontic microbiome is critical to the efficacy of endodontic treatment in diverse types of illness. We conducted a thorough and critical assessment of original research articles that looked into the microbiota of pulp and periapical infections for this study. Primary apical periodontitis, secondary apical periodontitis, and apical abscess are the endodontic diseases included in this study. Materials and Methods: The PRISMA statement and Cochrane criteria for systematic reviews were followed in the preparation of this systematic review’s methodology. For works published between 2000 and 2020, a thorough literature search was undertaken independently by two researchers in the PubMed, SCOPUS, and EMBASE databases. We found all of the papers that contained original data on oral microorganisms in pulp and periapical diseases. Anecdotal evidence, case reports, and reviews were excluded from the study. The complete text of 36 articles that satisfied the inclusion criteria were retrieved and reviewed for sample methodology, sequencing strategy, and microbiome makeup. All 36 publications were critically examined independently by three authors, following the Joanna Briggs Institute Reviewer’s Manual of 2017. Results: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most common phyla represented. Conclusion: All infection types are associated with an exceedingly diverse microbiome. These studies together map out an exhaustive chart of the taxa inherent in endodontic infections.

Keywords: Oral microbiome, pulp and periapical infections, systematic review

How to cite this article:
Benny B, Pillai VR, Joseph A, Pazhani J, Mony V. Oral Microbes Associated with Pulp and Periapical Infections. J Orofac Sci 2022;14:52-61

How to cite this URL:
Benny B, Pillai VR, Joseph A, Pazhani J, Mony V. Oral Microbes Associated with Pulp and Periapical Infections. J Orofac Sci [serial online] 2022 [cited 2023 Jun 9];14:52-61. Available from:

  Introduction Top

Bacteria infiltrating the tooth pulp and root canal system produce apical periodontitis, an inflammatory condition of the dental periapical tissues. Bacterial invasion of the root canals (endodontic infection) occurs as a result of caries, trauma, or periodontal disease, and invariably results in tissue necrosis. Complex bacterial communities colonize necrotized root canals quickly, reach the connective tissues surrounding the teeth through the apical foramen, and cause “primary apical periodontitis” (PAP), a periapical lesion. PAP lesions can be treated using an endodontic procedure that focuses on removing the pathogenic bacteria from the root canals. Untreated root canals, on the other hand, maintain persistent bacterial colonies that cause a periapical disease known as “secondary apical periodontitis” (SAP). The creation of a purulent accumulation known as an “apical abscess” (AA) may occur as a result of PAP and SAP lesions. All three types of endodontic infections (PAPs, SAPs, and AAs) produce inflammation, alveolar bone loss, and the potential for life-threatening infections. This knowledge should lead to the development of a framework for improving current therapy regimens and lowering the prevalence of persistent endodontic infections.[1]

The goal of this study was to analyze articles that looked into the microbiome of pulp and periapical infections in a systematic and critical manner. The microbiota composition in PAPs, SAPs, and AAs was examined as the outcome of interest. The type of endodontic infections, bacterial sampling methodology, sequencing technology, and microbiome composition were all evaluated in the selected articles.

  Materials and Methods Top

The PRISMA declaration and the Cochrane principles for systematic reviews (version 5.1.0; http: / were followed in the execution of this systematic review.[2]

Inclusion Criteria

A thorough literature search for English literature publications published between 2000 and 2020 was done independently by two researchers in the PubMed, SCOPUS, and EMBASE databases. We included all studies with unique data on oral microorganisms in pulp and periapical infections.

Exclusion Criteria

All duplicates and articles with only an abstract were eliminated. Anecdotal evidence, case reports, and reviews were excluded from the study. Articles published in language other than English, grey literature, and studies done on deciduous teeth were also excluded.

Sources, Search Strategy, and Study Selection

A literature search was performed using PubMed, SCOPUS, and EMBASE databases to identify original articles that investigated microbiota of infected root canal systems. The search strategy included three distinct blocks of keyword. Block 1: “microbiome” OR “microbiota” (MeSH term) OR “bacterial composition.” Block 2: “dental pulp cavity” (MeSH term) OR “primary apical periodontitis” OR “secondary apical periodontitis” OR “periapical periodontitis” (MeSH term) OR “endodontic infection.” Block 3: “DNA hybridization” OR “high throughput sequencing” OR “pyrosequencing” OR “PCR.” The final search combined the three blocks each searched by two researchers AND to collect articles that incorporated all the three blocks of interest.

From the databases, a total of 355 potentially relevant papers containing information on oral microorganisms in pulp and periapical infections were found, with 316 articles being removed after a review of the title and abstract. The complete text of 36 articles that met the inclusion criteria was obtained [Table 1].
Table 1 List of original research articles included in the study

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Data Extraction and Management

The authors evaluated and reviewed the data in this review, which covered the type of endodontic infections, bacterial sample methodology, sequencing technology, and microbiota makeup.

Risk of Bias and Quality Assessment of Studies

The publications were critically appraised separately by three authors in accordance with the Joanna Briggs Institute Reviewer’s Manual of 2017 ( for analytical cross-sectional studies.

  Results and Discussion Top

Different types of endodontic infections investigated

The diagnosis of endodontic infections analyzed could be classified as PAP, SAP, or AA in all of the studies included. PAP lesions were assessed in 23 articles, SAP lesions in 14 articles, and AAs in three articles.

Bacterial sampling methodology

Sampling methodologies used in these studies can be classified as in vivo or ex vivo. The noninvasive paper point (in vivo) sampling approach preserves the concerned tooth. The disadvantage of the paper point sample approach is its inability to reach the apical region, limiting the sampling to bacteria from the main root canal in some cases. Furthermore, without discriminating between the coronal and apical regions of the root canal, this approach merely provides an average impression of the taxa present. Cryo-pulverization (ex vivo), on the other hand, enables the selective examination of the microbiome found in the apical region of the root, as well as the sampling of biofilm communities entrapped in radicular abnormalities. One major disadvantage of cryo-pulverization is that it frequently necessitates tooth extraction, which is why it is preferred in extremely infected and recalcitrant cases.[1] The majority of the investigations (31/36 studies) used an in vivo sample strategy, which involved inserting paper points into the root canal during endodontic treatment to acquire the root microbiota. In these cases, the teeth investigated were retained in the oral cavity. Two of the investigations (two/36 studies) used an ex vivo sampling strategy, which involved extracting the roots before studying the microbiota. Cryo-pulverization of root sections, a process for sectioning the apical region of the root and subsequently grinding it at liquid nitrogen temperatures in customized freezer mills, was employed in this research. The studies used needle aspiration of pus in cases of AAs (three/36 studies).

Sequencing strategy

DNA–DNA Hybridization Technique

The checkerboard DNA–DNA hybridization method was developed for hybridizing huge numbers of DNA samples against large numbers of DNA probes on a single support membrane. It allows for the simultaneous detection of a large number of bacterial species in a single or many clinical samples. The approach is particularly useful in epidemiologic research since it does not require bacterial viability. Molecular approaches, in contrast to traditional culture procedures, do not rely on sampling under tightly controlled anaerobic conditions, do not require special transport media, and do not necessitate the development of isolates. These benefits ensure the detection of germs that are either uncultivable or difficult to grow. The technology of DNA–DNA hybridization has the added benefit of not amplifying DNA. Microbial contaminants are not cultured or their DNA amplified as a result. Furthermore, while negative results suggest that the target bacteria were either absent or present in quantities below the detection threshold, the chance that some target species were present but not detected cannot be ruled out.[3]
Figure 1 PRISMA flow chart of literature search.[2]

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Polymerase chain reaction assays

Polymerase chain reaction (PCR) assays are extremely sensitive, allowing for the accurate identification of microbial species or strains that are difficult to cultivate, if not impossible.[5] Furthermore, PCR is more sensitive than culture and may be less affected by chemical variables, such as leftovers of drugs that can enter a sample and impede microbial growth in the lab.[6] The PCR has made a substantial contribution to our understanding of endodontic microbiota associated with primary infections because it can overcome several intrinsic limitations of culture.[5] One of the PCR assay’s potential drawbacks is that it does not produce quantifiable results. As a result, determining whether discovered species appeared in sufficient quantities to engage in the infectious process is difficult.[6]

New generation sequencing

The microbiota of infected roots was traditionally studied using culture and close-ended molecular approaches such as PCR (and derivatives) and DNA hybridization assays until the advent of new generation sequencing (NGS) technologies. These more traditional methods allowed researchers to only index a group of 20 to 30 bacterial species that are thought to be important in the etiology of PAP and SAP lesions. In comparison, NGS investigations found on average 400 OTUs (species-level taxa) in infected root canals, which were not confined to these strains that can be cultivated in the laboratory or to a range of predefined species.[1]

Microbiota composition in pulp and periapical infections

Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most common phyla encountered, regardless of infection type. We have compiled a list of notable bacterial profiles, with key discoveries grouped by the kind of endodontic infection.

Primary apical periodontitis

Enterococcus faecalis was the most common species in four of the 23 PAP studies. This could indicate that the species is a secondary opportunistic colonizer, not part of the microbiome present in PAP prior to therapy. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most commonly detected phyla. In addition to this, a few researches discovered some specific microorganisms. The most common species found by Schirrmeister et al.[11] were Solobacterium moorei and Fusobacterium nucleatum. Peptostreptococcus was the most common species, followed by Streptococcus, Porphyromonas, and E. faecalis, according to Gajan et al.’s[13] study. Propionibacterium acnes (52%), F. nucleatum subspecies nucleatum (24%), Streptococcus species (17%), Propionibacterium acidifaciens (14%), Pseudoramibacter alactolyticus (14%), E. faecalis (12%), and Tannerella forsythia (12%) were the most common taxa in a later study by Rôças et al.[19] Representatives of the genera Lactobacillus, Actinomyces, Streptococcus, and Prevotella were detected in all samples in the study by Özok et al.[20] According to Pereira et al.,[33] the bacterial population in both the root ends and periapical tissues comprised of: F. nucleatum (71.6%) > Dialister pneumosintes (58.3%) > T. forsythia (48.3%) > Aggregatibacter actinomycetemcomitans (25%).

Secondary apical periodontitis

According to Siqueira et al.[5] and Barbosa-Ribeiro et al.,[38] E. faecalis was the most often recovered bacterial species. Rôças et al.[9] discovered that Streptococcus species (47%) and Lactobacillus species (35%) were the most often observed taxa. Fusobacterium spp. were the most common in the study by Handal et al.[12] Firmicutes (29.9%), Proteobacteria (26.1%), Actinobacteria (22.72%), and Bacteroidetes (13.31%) were the most prevalent phyla, according to Anderson et al.[21] Staphylococcus spp. (13.63%), Actinomyces spp. (12.72%), Gemella spp. (10.9%), Haemophilus spp. (9.09%), and Enterococcus spp. (7.27%) were the bacterial species most often recovered from root canals, according to Endo et al.[22] Proteobacteria (46%), Firmicutes (18%), Fusobacteria (15%), and Actinobacteria (8%) were the most common phyla, according to Siqueira et al.[28] Firmicutes, Fusobacteria, Bacteroidetes, and Actinobacteria were the most abundant and prevalent phyla in the study by Zandi et al.[31] Proteobacteria was the most prevalent phylum, followed by Bacteroidetes, according to Sánchez-Sanhueza et al.[35] According to Zargar et al.,[37] E. faecalis and Dialister invisus were the most abundant species.

The bacterium E. faecalis was the most frequently found in root canals associated with SAP. Firmicutes were the most common phylum discovered.

Apical abscess

Bacteroides forsythus (29.6%), Porphyromonas gingivalis (29.6%), Streptococcus constellatus (25.9%), Prevotella intermedia (22.2%), and Prevotella nigrescens (22.2%) were the most common, according to Siqueira et al.[3] Prevotella species, oral streptococci, Corynebacterium species, staphylococci, and Peptostreptococcus species were the most common, according to Khemaleelakul et al.[4] F. nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis were the most prevalent bacteria in a later investigation by George et al.[29]

One drawback of this study was that in 31 out of the 36 articles shortlisted, paper point sampling was the method employed, which limited the study of the microbes within the root canal to the main canal only and the microbes present within the accessory canals were not retrieved. Also, the more traditional sequencing methods like PCR and DNA–DNA hybridization allowed researchers to only index a group of 20 to 30 bacterial species that are thought to be important in the etiology of PAP and SAP lesions.

As the microbial population is constantly evolving and adapting to the changing environment that it encounters, it is imperative that research in this field should be pursued in the future as well to stay abreast of the developing microbiota. Only this will allow a dental practitioner to employ proper treatment procedures and medicaments to combat the microbiome.

  Conclusion Top

The findings of this study corroborate the existing theory that pulp and periapical pathologies are caused by a polymicrobial etiology. The number of identifiable species associated with endodontic infections has increased due to advances in molecular technologies. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most prevalent phyla. The species E. faecalis was the most frequently found in SAPs-related root canals. Deciphering the composition of the microbiota associated with root canal infection is of utmost importance not only for a better understanding of the disease pathogenesis, but also for establishing more effective therapeutic protocols. Treatment strategies should aim at thorough elimination of the microbiota residing in infected root canal, with a focus on disturbing the ecosystem to prevent the survival of bacterial community. Additionally, alternative measures to eradicate resistant microorganisms, such as passive ultrasonic irrigation, apical negative pressure irrigation systems, and ozone gas may provide helpful treatment options in addition to chemo-mechanical preparation.

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Conflicts of interest

There are no conflicts of interest.

  References Top

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