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Park DH, Park OJ, Yoo YJ, Perinpanayagam H, Cho EB, Kim K, Park J, Noblett WC, Kum KY, Han SH. Microbiota Association and Profiling of Gingival Sulci and Root Canals of Teeth with Primary or Secondary/Persistent Endodontic Infections. J Endod 2024:S0099-2399(24)00279-6. [PMID: 38768706 DOI: 10.1016/j.joen.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Microbiota associated with primary endodontic infection (PEI) and secondary/persistent endodontic infection (SPEI) must be characterized to elucidate pathogenesis in apical periodontitis and bacterial biomarkers identified for diagnostic and therapeutic applications. METHODS This study analyzed the microbial community profiles of root canals and gingival sulci (sulcus-E) for teeth with PEI (n = 10) or SPEI (n = 10), using the Illumina MiSeq platform. Bacterial samples from gingival sulci (sulcus-C) of healthy contralateral teeth served as controls. RESULTS There were 15 phyla, 177 genera, and 340 species identified. The number and diversity of bacteria in root canals did not differ significantly between PEI and SPEI. Proteobacteria, Firmicutes, Fusobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in both groups. At the genus level, Lancefieldella, Bifidobacterium, Stomatobaculum, and Schaalia were enriched in root canals with SPEI. Of significance, Lancefieldella was observed in both root canals and sulcus-E of teeth with SPEI. At the species level, Neisseria macacae, Streptococcus gordonii, Bifidobacterium dentium, Stomatobaculum longum, and Schaalia odontolytica were increased significantly in root canals with SPEI compared to PEI. Oribacterium species, Streptococcus salivarius, Lancefieldella parvula, Prevotella denticola, and Oribacterium asaccharolyticum were more abundant in sulcus-E of teeth with SPEI compared to PEI. CONCLUSIONS There were distinctive and differing predominant bacterial species associated with the root canals and gingival sulci between teeth with PEI and SPEI. Specific bacteria identified in sulcus-E and root canals of teeth with SPEI could serve as noninvasive diagnostic biomarkers for detecting SPEI.
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Affiliation(s)
- Dong Hyun Park
- Department of Oral Microbiology and Immunology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Ok-Jin Park
- Department of Oral Microbiology and Immunology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Yeon-Jee Yoo
- Department of Conservative Dentistry, Dental Research Institute, Seoul National University Dental Hospital, Seoul National University School of Dentistry, Seoul, Republic of Korea
| | - Hiran Perinpanayagam
- Division of Endodontics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Eun-Bee Cho
- Department of Conservative Dentistry, Dental Research Institute, Seoul National University Dental Hospital, Seoul National University School of Dentistry, Seoul, Republic of Korea
| | | | | | - W Craig Noblett
- Division of Endodontics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota
| | - Kee-Yeon Kum
- Department of Conservative Dentistry, Dental Research Institute, Seoul National University Dental Hospital, Seoul National University School of Dentistry, Seoul, Republic of Korea.
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea.
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Pinheiro ET, Karygianni L, Candeiro GTM, Vilela BG, Dantas LO, Pereira ACC, Gomes BPFA, Attin T, Thurnheer T, Russo G. Metatranscriptome and Resistome of the Endodontic Microbiome. J Endod 2024:S0099-2399(24)00276-0. [PMID: 38719087 DOI: 10.1016/j.joen.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 06/07/2024]
Abstract
INTRODUCTION In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections. METHODS Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification. RESULTS Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms. CONCLUSIONS Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.
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Affiliation(s)
- Ericka T Pinheiro
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil; Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland.
| | - Lamprini Karygianni
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - George T M Candeiro
- Faculty of Dentistry, Christus University Center (Unichristus), Fortaleza, Ceará, Brazil
| | - Bruna G Vilela
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Larissa O Dantas
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Ana C C Pereira
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Piracicaba, São Paulo, Brazil
| | - Thomas Attin
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - Thomas Thurnheer
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, ETH-University of Zurich, Zürich, Switzerland (previous affiliation); EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania; Institute of Bioscience, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Li Y, Shi P, Zhu R. A pulmonary abscess caused by Porphyromonas endodontalis infection:A case report and literature review. Diagn Microbiol Infect Dis 2024; 108:116126. [PMID: 37925846 DOI: 10.1016/j.diagmicrobio.2023.116126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Porphyromonas endodontalis is an oral anaerobic bacterium associated with periodontitis but seldomly been detected in other diseases. Only one case of respiratory disease caused by Porphyromonas endodontalis, pyopneumothorax, has been reported so far. A 53-year-old man with refractory periodontitis was admitted due to an indeterminate lung space-occupying lesion. Following mNGS analysis of the liquefaction necrotic area and solid component of the lesion through biopsy, Porphyromonas endodontalis and Parvimonas micra were detected. Therefore, the patient was diagnosed with an aspiration lung abscess and discharged after receiving effective antibacterial treatment. The Chest computed tomography (CT) scan revealed a remarkable improvement during outpatient follow-up. In this study, we applied mNGS to diagnose a case of lung abscess attributed to an uncommon bacterium successfully, suggesting that when patients complicated with periodontal diseases and clinical respiratory symptoms, the possibility of inhalation disease caused by oral pathogens should be considered.
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Affiliation(s)
- Yao Li
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian 223001, China
| | - Pengfei Shi
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian 223001, China
| | - Rong Zhu
- Department of Respiratory and Critical Care Medicine, Huaian Clinical College of Xuzhou Medical University, Huaian 223001, China.
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Hu Z, Xiang Y, Wei Y, Gu X, Leng W, Xia L. Bacterial diversity in primary infected root canals of a Chinese cohort: analysis of 16 S rDNA sequencing. BMC Oral Health 2023; 23:932. [PMID: 38012618 PMCID: PMC10680180 DOI: 10.1186/s12903-023-03618-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023] Open
Abstract
PURPOSE To characterize the bacterial community in the primarily infected root canals. METHODS A total of 13 samples were collected from the primarily infected root canals. 16 S rDNA sequencing was performed to define bacterial community. Taxonomic annotation, bacterial hierarchical structures, community richness and diversity, and inter-subject variability of the bacterial community in the root canal samples were analyzed. Gender, age, and duration of the toothache-specific bacterial community associated with the patient groups were analyzed. RESULTS A total of 359 Species were annotated and identified in the whole study cohort. The Alpha diversity analysis showed that the species diversity and detection rate of the 13 samples were high, which reflected the authenticity of sequencing results. The Beta diversity analysis was used to compare the degree of difference between different root canal samples. The 13 samples were divided into two groups according to the results, group A was samples I1-I12, and group B was samples I13. The bacterial species of group A samples were analyzed with the clinical characteristics of patients, and it was found that gender, and duration specific differences in bacterial species, and there was no significant difference in species types among different ages of patients. CONCLUSION There were a wide diversity and inter-subject variability in the bacterial community in the primary infected root canals. While Porphyromonas gingivalis was the most abundant species, Fusobacterium nucleatum was the most variable species in the bacterial community of the root canal. The bacterial community at different taxonomic levels varied from sample to sample, despite consistent disease diagnoses. There was gender, duration-specific differences in the bacterial species in the primary infected root canals.
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Affiliation(s)
- Ziqiu Hu
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
- Institute of Oral Diseases, School of Dentistry, Hubei University of Medicine, Shiyan, 442000, China
| | - Yonggang Xiang
- Department of Ophthalmology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yanhong Wei
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China
- Institute of Oral Diseases, School of Dentistry, Hubei University of Medicine, Shiyan, 442000, China
| | - Xinsheng Gu
- Department of Pharmacology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Weidong Leng
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China.
- Institute of Oral Diseases, School of Dentistry, Hubei University of Medicine, Shiyan, 442000, China.
| | - Lingyun Xia
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, China.
- Institute of Oral Diseases, School of Dentistry, Hubei University of Medicine, Shiyan, 442000, China.
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Antezack A, Etchecopar-Etchart D, La Scola B, Monnet-Corti V. New putative periodontopathogens and periodontal health-associated species: A systematic review and meta-analysis. J Periodontal Res 2023; 58:893-906. [PMID: 37572051 DOI: 10.1111/jre.13173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/14/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature searches in the MEDLINE (PubMed), EMBASE, DOSS and Google Scholar databases as well as a manual search to identify eligible clinical studies prior to November 2022. Studies comparing the prevalence of microorganisms other than the already-known periodontal pathogens in subgingival plaque and/or saliva samples between subjects with periodontitis and subject with periodontal health were included. Meta-analyses were performed on data provided by the included studies. Fifty studies including a total of 2739 periodontitis subjects and 1747 subjects with periodontal health were included. The Archaea domain and 25 bacterial species (Anaeroglobus geminatus, Bacteroidales [G-2] bacterium HMT 274, Desulfobulbus sp. HMT 041, Dialister invisus, Dialister pneumosintes, Eubacterium brachy, Enterococcus faecalis, Eubacterium nodatum, Eubacterium saphenum, Filifactor alocis, Fretibacterium sp. HMT 360, Fretibacterium sp. HMT 362, Mogibacterium timidum, Peptoniphilaceae sp. HMT 113, Peptostreptococcus stomatis, Porphyromonas endodontalis, Slackia exigua, Streptococcus gordonii, Selenomonas sputigena, Treponema amylovorum, Treponema lecithinolyticum, Treponema maltophilum, Treponema medium, Treponema parvum and Treponema socranskii) were found to be statistically significantly associated with periodontitis. Network studies should be conducted to investigate the role of these newly identified periodontitis-associated microorganisms through interspecies interaction and host-microbe crosstalk analyses.
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Affiliation(s)
- Angéline Antezack
- Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix-Marseille Univ, Marseille, France
- AP-HM, Hôpital Timone, Pôle Odontologie, Service de Parodontologie, Marseille, France
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Damien Etchecopar-Etchart
- EA 3279: CEREeSS-Health Service Research and Quality of Life Center, Aix-Marseille Univ, Marseille, France
- Département de Psychiatrie, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- FondaMental Foundation, Creteil, France
| | - Bernard La Scola
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Virginie Monnet-Corti
- Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix-Marseille Univ, Marseille, France
- AP-HM, Hôpital Timone, Pôle Odontologie, Service de Parodontologie, Marseille, France
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
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Alhadainy HA, Abdel-Karim AH, Fouad AF. Prevalence of Fusobacterium Species in Endodontic Infections Detected With Molecular Methods: Systematic Review and Meta-Analysis. J Endod 2023; 49:1249-1261. [PMID: 37611654 DOI: 10.1016/j.joen.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Endodontic infections are polymicrobial; however, investigating the role of bacterial species is critical because they may influence pathogenesis, the development of symptoms, or the persistence of disease. This systematic review aimed to determine the prevalence of Fusobacterium species and its association with different types of endodontic infections. METHODS MEDLINE (Ovid), PubMed, Scopus, Web of Science, and Cochrane Library databases were used as electronic databases to retrieve relevant studies. The studies were evaluated for eligibility criteria, and the certainty in evidence and risk of bias were evaluated using critical appraisal tools for prevalence studies from the Joanna Briggs Institute. Forty studies were selected for meta-analysis and statistically analyzed for the relationship between the prevalence of Fusobacterium species and both the presence of symptoms and the type of infections (primary vs secondary/persistent) using meta-regression analysis. RESULTS The prevalence of Fusobacterium spp. in endodontic infections ranged from 3%-100% (mean = 42.51%) in the 40 included studies. Calculated confidence intervals indicated that the presence of Fusobacterium spp. was not statistically associated with the presence of symptoms or with the type of infections (the set of 2 predictors was not significant; P < .05). CONCLUSIONS The prevalence of Fusobacterium infection, which was identified with molecular methods, was not significant for overall regression using both predictors (ie, symptoms [symptomatic vs asymptomatic] and types of infections [primary vs secondary/persistent]).
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Affiliation(s)
- Hatem A Alhadainy
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Ashraf F Fouad
- Department of Endodontics, University of Alabama at Birmingham, Birmingham, Alabama.
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Song Z, Fang S, Guo T, Wen Y, Liu Q, Jin Z. Microbiome and metabolome associated with white spot lesions in patients treated with clear aligners. Front Cell Infect Microbiol 2023; 13:1119616. [PMID: 37082715 PMCID: PMC10111054 DOI: 10.3389/fcimb.2023.1119616] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
White spot lesions (WSLs) have long been a noteworthy complication during orthodontic treatment. Recently, an increasing number of orthodontists have found that adolescents undergoing orthodontic treatment with clear aligners are at a higher risk of developing WSLs. The oral microbiota and metabolites are considered the etiologic and regulatory factors of WSLs, but the specific impact of clear aligners on the oral microbiota and metabolites is unknown. This study investigated the differences in the salivary microbiome and metabolome between adolescents with and without WSLs treated with clear aligners. Fifty-five adolescents (aged 11-18) with Invisalign appliances, 27 with and 28 without WSLs, were included. Saliva samples were analyzed using 16S rRNA gene sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); the data were further integrated for Spearman correlation analysis. The relative abundances of 14 taxa, including Actinobacteria, Actinomycetales, Rothia, Micrococcaceae, Subdoligranulum, Capnocytophaga, Azospira, Olsenella, Lachnoanaerobaculum, and Abiotrophia, were significantly higher in the WSL group than in the control group. Metabolomic analysis identified 27 potential biomarkers, and most were amino acids, including proline and glycine. The metabolites were implicated in 6 metabolic pathways, including alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism; and aminoacyl-tRNA biosynthesis. There was a correlation between the salivary microbial and metabolomic datasets, reflecting the impact of clear aligners on the metabolic activity of the oral flora. A concordant increase in the levels of Lachnoanaerobaculum, Rothia, Subdoligranulum and some amino acids had predictive value for WSL development. In summary, when adolescents undergo long-term clear aligner therapy with poor oral hygiene habits, clear aligners can disrupt the balance of the oral microecosystem and lead to oral microbiota dysbiosis, thereby increasing the risk of developing WSLs. Our findings might contribute to the understanding of the pathogenesis of WSLs and provide candidate biomarkers for the diagnosis and treatment of WSLs associated with clear aligners.
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Affiliation(s)
- Zhixin Song
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi’an, China
| | - Shishu Fang
- Department of Stomatology, General Hospital of Southern Theater Command of the Chinese People’s Liberation Army, Guangzhou, China
| | - Tao Guo
- Department of Orthodontics, TaiKang Shanghai Bybo Dental Hospital, Shanghai, China
| | - Yi Wen
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi’an, China
| | - Qian Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi’an, China
- *Correspondence: Qian Liu, ; Zuolin Jin,
| | - Zuolin Jin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, Air Force Medical University, Xi’an, China
- *Correspondence: Qian Liu, ; Zuolin Jin,
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Kesim B, Ülger ST, Aslan G, Cudal H, Üstün Y, Küçük MÖ. Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections. Clin Oral Investig 2023; 27:995-1004. [PMID: 36723715 DOI: 10.1007/s00784-023-04882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 01/24/2023] [Indexed: 02/02/2023]
Abstract
OBJECTIVES To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm. MATERIALS AND METHODS Root canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0. RESULTS Within the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group. CONCLUSIONS A few taxa were differentially abundant within either the PEI or SEI group. CLINICAL RELEVANCE Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections.
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Affiliation(s)
- Bertan Kesim
- Department of Endodontics, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey. .,Kuzey Çevreyolu Erkilet Dere Mah, Nuh Naci Yazgan Üniversitesi Yerleşkesi, Kocasinan, Kayseri, Turkey.
| | - Seda Tezcan Ülger
- Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Gönül Aslan
- Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Hamza Cudal
- Department of Endodontics, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey
| | - Yakup Üstün
- Department of Endodontics, Faculty of Dentistry, Erciyes University, Kayseri, Turkey
| | - Mustafa Öner Küçük
- Department of Microbiology, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey
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Astorga J, Hernández M, Bravo D, Hoare A. Evaluation of PCR primers to identify Porphyromonas endodontalis in apical periodontitis clinical samples. Arch Microbiol 2022; 204:652. [PMID: 36173466 DOI: 10.1007/s00203-022-03260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2022]
Abstract
We aimed to evaluate whether two commonly used PCR primers are effective to identify P. endodontalis and discriminate from other prevalent black-pigmented bacteria in apical periodontitis (AP). Endodontic canal samples from patients with asymptomatic AP (n = 20) were collected and cultured in anaerobiosis. Two primer sets to detect P. endodontalis were selected from the literature and first analyzed for their specificity in silico; and then tested on clinical isolates in vitro and finally, in apical exudates ex vivo. The identity of P. endodontalis was verified by PCR and Sanger sequencing with universal primers for bacterial V3-V6 regions 16S rDNA. Only one primer set showed specificity only for P. endodontalis clones in silico and also was specific for P. endodontalis in vitro and ex vivo.
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Affiliation(s)
- J Astorga
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Olivos 943, 8380492, Independencia, 8380000, Santiago, Chile
| | - M Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Olivos 943, 8380492, Independencia, 8380000, Santiago, Chile.,Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Olivos 943, 8380492, Independencia, 8380000, Santiago, Chile
| | - D Bravo
- Laboratory of Oral Microbiology, Department of Pathology and Oral Medicine, Faculty of Dentistry, Olivos 943, 8380492, Independencia, 8380000, Santiago, Chile
| | - A Hoare
- Laboratory of Oral Microbiology, Department of Pathology and Oral Medicine, Faculty of Dentistry, Olivos 943, 8380492, Independencia, 8380000, Santiago, Chile.
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Könönen E, Fteita D, Gursoy UK, Gursoy M. Prevotella species as oral residents and infectious agents with potential impact on systemic conditions. J Oral Microbiol 2022; 14:2079814. [DOI: 10.1080/20002297.2022.2079814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Eija Könönen
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Dareen Fteita
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi K. Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Mervi Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
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Nardello LCL, Pinheiro ET, Gavini G, Prado LC, Romero RX, Gomes BPFA, Skelton-Macedo MC. Nature and Prevalence of Bacterial Taxa Persisting after Root Canal Chemomechanical Preparation in Permanent Teeth: A Systematic Review and Meta-analysis. J Endod 2022; 48:572-596. [PMID: 35114271 DOI: 10.1016/j.joen.2022.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/15/2022] [Accepted: 01/21/2022] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Culture-independent molecular studies have shown a broad spectrum of bacterial taxa that persist after chemomechanical procedures (CMP). Therefore, this study systematically reviewed these reports to explore the prevalence of bacteria in post-instrumentation samples of root canals from permanent teeth, especially of as-yet-uncultivated/difficult-to-culture bacteria. METHODS Electronic databases were searched from 2007 to January 2021. Clinical studies using culture-independent molecular methods to identify species-level taxa before and after CMP were included. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist and the funnel plot analysis. The meta-analysis was performed on the prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa using RStudio. RESULTS A total of 3781 titles were screened, but only 20 studies were included. The most frequent species in post-instrumentation samples were Streptococcus spp., Leptotrichia buccalis, Fusobacterium nucleatum, and Capnocytophaga ochracea. The detection frequency of some species increased after CMP, including mainly Firmicutes members such as streptococci, Enterococcus faecium, Selenomonas noxia, and Solobacterium moorei. The prevalence (confidence interval) of difficult-to-culture species was as follows: Dialister invisus, 17% (7%-29%); Solobacterium moorei, 14% (8%-23%); Bacteroidaceae [G-1] bacterium HMT 272, 13% (5%-23%); and Filifactor alocis, 11% (3%-23%). CONCLUSIONS The prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa in post-instrumentation samples was low. The persistent species belonged mainly to the phylum Firmicutes, and streptococci were the major members. Future larger clinical studies on the composition of the whole bacterial community that persist after CMP are still necessary for a better understanding of bacterial interactions and their clinical significance in the treatment outcome.
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Affiliation(s)
- Laura C L Nardello
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Ericka T Pinheiro
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil.
| | - Giulio Gavini
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Laís C Prado
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Roberto X Romero
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil
| | - Mary C Skelton-Macedo
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
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12
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Boutsioukis C, Arias-Moliz MT, Chávez de Paz LE. A critical analysis of research methods and experimental models to study irrigants and irrigation systems. Int Endod J 2022; 55 Suppl 2:295-329. [PMID: 35171506 PMCID: PMC9314845 DOI: 10.1111/iej.13710] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
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-omputed 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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Affiliation(s)
- C Boutsioukis
- Department of Endodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M T Arias-Moliz
- Department of Microbiology, Faculty of Dentistry, University of Granada, Granada, Spain
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Amaral RR, Braga T, Siqueira JF, Rôças IN, da Costa Rachid CTC, Guimarães Oliveira AG, de Souza Côrtes MI, Love RM. Root Canal Microbiome Associated with Asymptomatic Apical Periodontitis as Determined by High-Throughput Sequencing. J Endod 2022; 48:487-495. [DOI: 10.1016/j.joen.2022.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 12/15/2022]
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14
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Siqueira JF, Rôças IN. A critical analysis of research methods and experimental models to study the root canal microbiome. Int Endod J 2021; 55 Suppl 1:46-71. [PMID: 34714548 DOI: 10.1111/iej.13656] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
| | - Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
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Tian XY, Xing JW, Zheng QQ, Gao PF. 919 Syrup Alleviates Postpartum Depression by Modulating the Structure and Metabolism of Gut Microbes and Affecting the Function of the Hippocampal GABA/Glutamate System. Front Cell Infect Microbiol 2021; 11:694443. [PMID: 34490139 PMCID: PMC8417790 DOI: 10.3389/fcimb.2021.694443] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
Postpartum depression (PPD) is a mental disorder that affects pregnant women around the world, with serious consequences for mothers, families, and children. Its pathogenesis remains unclear, and medications for treating PPD that can be used during lactation remain to be identified. 919 syrup (919 TJ) is a Chinese herbal medicine that has been shown to be beneficial in the treatment of postpartum depression in both clinical and experimental studies. The mechanism of action of 919 TJ is unclear. 919 syrup is ingested orally, making the potential interaction between the drug and the gut microbiome impossible to ignore. We therefore hypothesized that 919 syrup could improve the symptoms of postpartum depression by affecting the structure and function of the intestinal flora, thereby altering hippocampal metabolism. We compared changes in hippocampal metabolism, fecal metabolism, and intestinal microflora of control BALB/c mice, mice with induced untreated PPD, and mice with induced PPD treated with 919 TJ, and found that 4-aminobutyric acid (GABA) in the hippocampus corresponded with PPD behaviors. Based on changes in GABA levels, multiple key gut bacterial species (Mucispirillum schaedleri, Bifidobacterium pseudolongum, Desulfovibrio piger, Alloprevotella tannerae, Bacteroides sp.2.1.33B and Prevotella sp. CAG:755) were associated with PPD. Metabolic markers that may represent the function of the intestinal microbiota in mice with PPD were identified (Met-Arg, urocanic acid, thioetheramide-PC, L-pipecolic acid, and linoleoyl ethanolamide). The relationship between these factors is not a simple one-to-one correspondence, but more likely a network of staggered functions. We therefore believe that the composition and function of the entire intestinal flora should be emphasized in research studying the gut and PPD, rather than changes in the abundance of individual bacterial species. The introduction of this concept of “GutBalance” may help clarify the relationship between gut bacteria and systemic disease.
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Affiliation(s)
- Xin-Yun Tian
- Department of Traditional Chinese Medicine, Jinshan Hospital of Fudan University, Shanghai, China
| | - Jing-Wei Xing
- Department of Traditional Chinese Medicine, Jinshan Hospital of Fudan University, Shanghai, China
| | - Qiao-Qi Zheng
- Department of Traditional Chinese Medicine, Jinshan Hospital of Fudan University, Shanghai, China
| | - Peng-Fei Gao
- Department of Traditional Chinese Medicine, Jinshan Hospital of Fudan University, Shanghai, China
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Schulz-Weidner N, Weigel M, Turujlija F, Komma K, Mengel JP, Schlenz MA, Bulski JC, Krämer N, Hain T. Microbiome Analysis of Carious Lesions in Pre-School Children with Early Childhood Caries and Congenital Heart Disease. Microorganisms 2021; 9:microorganisms9091904. [PMID: 34576799 PMCID: PMC8469307 DOI: 10.3390/microorganisms9091904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/23/2021] [Accepted: 09/02/2021] [Indexed: 12/04/2022] Open
Abstract
Oral bacteria have been associated with several systemic diseases. Moreover, the abundance of bacteria associated with caries has been found to be higher in patients with congenital heart disease (CHD) than in healthy control groups (HCGs). Therefore, this study aimed to evaluate the dental microbiota in children with CHD compared to a HCG. The aim was to describe and compare the carious microbiome regarding the composition, diversity, and taxonomic patterns in these two groups. Twenty children with CHD and a HCG aged between two and six years participated. All of them were affected by early childhood caries. Microbiome profiling indicated that Fusobacterium, Prevotella, Capnocytophaga, and Oribacterium were more abundant in the CHD group, whereas Lactobacillus and Rothia were predominant in the HCG. Furthermore, microbiome analysis revealed three distinct clusters for the CHD and HCG samples. In the first cluster, we found mainly the genera Lactobacillus and Coriobacteriaceae. The second cluster showed a higher relative abundance of the genus Actinomyces and a more diverse composition consisting of more genera with a smaller relative lot. The third cluster was characterized by two genera, Streptococcus and Veillonella. These data can help us to understand the oral microbial community structures involved in caries and endodontic infections of pre-school children in relation to the general health of these high-risk patients.
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Affiliation(s)
- Nelly Schulz-Weidner
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Markus Weigel
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Filip Turujlija
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Kassandra Komma
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Jan Philipp Mengel
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Maximiliane Amelie Schlenz
- Dental Clinic—Department of Prosthodontics, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany;
| | - Julia Camilla Bulski
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Norbert Krämer
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
- Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany
- Correspondence: ; Tel.: +49-641-9939860
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Nardello LC, Vilela BG, Fernandes FS, Bruno FP, Carvalho AP, Cazares RX, Nascimento LC, Honório HM, Ando ES, Mayer MP, Gavini G, Pinheiro ET. Analysis of Active Bacteria Persisting after Chemomechanical Procedures: An RNA- and DNA-based Molecular Study. J Endod 2020; 46:1570-1576. [DOI: 10.1016/j.joen.2020.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
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