Detection of the unknown components of the oral microflora of teeth with periapical radiolucencies in a Turkish population using next‐generation sequencing techniques

İriboz, Emre; Arıcan, Burçin; Kolukırık, Mustafa; Karacan, Ilker; Öveçoğlu, Hesna Sazak

doi:10.1111/iej.12956

Cited by 14 publications

(15 citation statements)

References 35 publications

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“…Sampling methodologies employed in these studies can be separated into in vivo or ex vivo. The majority of the studies (11/18) used an in vivo sampling strategy, by which the root microbiota was collected using paper points inserted into the root canal during the course of an endodontic treatment . In these cases, the teeth investigated were to be retained in the oral cavity.…”

Section: Resultsmentioning

confidence: 99%

“…An example is provided herein by Iriboz et al. who treated their samples with DNase I, in order to degrade free DNA prior to extraction, and further evaluated the microbiota that resisted root canal disinfection . Aside from these specific research instances, evidence suggests that the half‐life of free DNA in the microbial environment of an infected root canal is very short and therefore unlikely to represent a major ratio of the DNA isolated .…”

Section: Discussionmentioning

confidence: 99%

“…Iriboz et al. were judged at “high risk” because they only reported the abundance of OTUs that varied before and after a root canal disinfection protocol . Whereas this display corresponds to the authors’ aim, it prevents the visualization of the complete community compositions and therefore affects the outcome of interest of this systematic review.…”

Section: Discussionmentioning

confidence: 99%

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

Manoil

Al‐Manei

Belibasakis

2020

Proteomics Clinical Apps

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Next-generation sequencing (NGS) has now been applied for a decade to characterize the microbiota composition of infected dental root canals associated with apical periodontitis. Here, the study aims at systematically and critically reviewing these reports within the outcome of interest selected; the microbiota composition in different endodontic infection types. Standard methodological guidelines as stated by the PRISMA and the Joanna Briggs Institute are followed, including a risk of bias assessment. A literature search is conducted using the PubMed Advanced-Search Builder on April 8, 2019; only original research articles that investigated the microbiota of infected root-canals by means of NGS are screened. Among the 26 articles initially identified, 18 are included and evaluated for the following parameters; sampling protocol, sequencing strategy, and microbiota composition. The endodontic infections include primary apical periodontitis (PAP), secondary apical periodontitis (SAP), and apical abscess (AA). All infection types are associated with a highly diverse microbiota. Although some taxa appear differentially abundant between PAPs, SAPs, and AAs, no evident clustering of the microbiota by infection type is observed. These studies collectively formulate a comprehensive map of the taxa associated with endodontic infections and provide evidence of compositionally unspecific, yet abundance differentiates, community profiles according to clinical diagnosis.The ORCID identification number(s) for the author(s) of this article can be found under https://doi.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Manoil

Al‐Manei

Belibasakis

2020

Proteomics Clinical Apps

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“…To amplify the V3-V4 hypervariable regions, the 341F/805R universal primers were used (43). A two-step Polymerase Chain Reaction (PCR) method was used to first amplify the target region and then to attach a barcode to each sample before pooling them for sequencing.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the oral microbiome of medically controlled type-2 diabetes patients

Santos

Martins-Mendes

Gayà-Vidal

et al. 2020

Preprint

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28Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a 29 significant global health care problem. Several studies have shown that people with 30 diabetes are more susceptible to oral problems, such as periodontitis and, although the 31 causes are still inconclusive, the oral microbiota seems to be an important factor in this 32 interaction. This study aimed to characterize the oral microbiome of a sample representing 33 T2DM patients from Portugal and exploit potential associations between some 34 microorganisms and variables like teeth brushing, smoking habits, and nutrient intake. 35 By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals 36 belonging to a group of diabetes patients and a control group, we found a total of 233 37 taxa, from which only 65% were shared between both groups. No differences were found 38 in terms of alpha and beta diversity between groups or habits categories. Also, there were 39 no significant differences in the oral microbiome profiles of control and diabetes patients. 40Only the class Synergistia and the genus TG5, which are related to periodontitis, were 41 statistically more frequent in the control group. This finding can be justified by the fact 42 that these diabetic patients usually have their oral health under close medical control than 43 an average healthy person, which in this study was represented by the control group. 44 45 IMPORTANCE: Diabetes has become a significant global health care issue as its 46 incidence continues to increase exponentially, with type 2 diabetes being responsible for 47 more than 90% of these cases. Portugal is one of the countries with a higher prevalence 48 of diabetes in Europe. It has been reported that diabetic people have an increased risk of 49 developing several health problems such as oral infections mostly caused by opportunistic 50 pathogens. Some studies have pointed out a relationship between diabetes and oral 51 3 microbiome. Therefore, the characterization of the microbial ecosystem of the mouth in 52 reference groups is crucial to provide information to tackle oral health pathogen-borne 53 conditions. In this study, we provide the first characterization of the oral microbiome of 54 type 2 diabetes mellitus patients from Portugal, and therefore, contributing new data and 55 knowledge to elucidate the relationship between diabetes and the oral microbiome. 56 57 58 59 60 61 62 Keywords: oral microbiome, type 2 diabetes mellitus, 16S rRNA gene sequencing, 63 microbiota, Next-Generation Sequencing, Portugal 64 65 67hyperglycemia caused by defects in insulin secretion, which can contribute to the 68 development of resistance to its action (1, 2). T2DM is becoming more common, also in 69 children and adolescents, and therefore, represents a significant global health care 70 problem (3). 71As more studies are focused on the impact of T2DM on the medium-term patients' health, 72 a growing number of studies have been reporting a close association between diabetes 73 and susce...

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“…Some studies reported that the half‐life of free DNA in an infected root canal seems to be very short because of the action of DNases and, therefore, it has only a minor effect on bacteria quantification by qPCR (Siqueira, 2008) but others have come to the conclusion that this DNA can be preserved for months, so it can be an important source of error (Brundin et al, 2014, 2015; Young et al, 2007). To overcome this problem, pre‐processing to degrade the free DNA prior to qPCR has been proposed (İriboz et al, 2018). This can be achieved by DNase treatment during sample preparation (İriboz et al, 2018).…”

Section: Antimicrobial Effectmentioning

confidence: 99%

A critical analysis of research methods and experimental models to study irrigants and irrigation systems

Boutsioukis

Arias-Moliz

Paz³

2022

Int Endodontic J

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Irrigation plays an essential role in root canal treatment. The purpose of this narrative review was to critically appraise the experimental methods and models used to study irrigants and irrigation systems and to provide directions for future research. Studies on the antimicrobial effect of irrigants should use mature multispecies biofilms grown on dentine or inside root canals and should combine at least two complementary evaluation methods. Dissolution of pulp tissue remnants should be examined in the presence of dentine and, preferably, inside human root canals. Micro‐computed tomography is currently the method of choice for the assessment of accumulated dentine debris and their removal. A combination of experiments in transparent root canals and numerical modeling is needed to address irrigant penetration. Finally, models to evaluate irrigant extrusion through the apical foramen should simulate the periapical tissues and provide quantitative data on the amount of extruded irrigant. Mimicking the in vivo conditions as close as possible and standardization of the specimens and experimental protocols are universal requirements irrespective of the surrogate endpoint studied. Obsolete and unrealistic models must be abandoned in favour of more appropriate and valid ones that have more direct application and translation to clinical Endodontics.

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Detection of the unknown components of the oral microflora of teeth with periapical radiolucencies in a Turkish population using next‐generation sequencing techniques

Abstract: The combination of NGS and qPCR techniques resulted in detection of previously unknown components of the oral microbiome and the effects of root canal treatment on their relative abundance in a Turkish population.

Cited by 14 publications

References 35 publications

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

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

Characterization of the oral microbiome of medically controlled type-2 diabetes patients

A critical analysis of research methods and experimental models to study irrigants and irrigation systems

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