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Siqueira JF, Silva WO, Romeiro K, Gominho LF, Alves FRF, Rôças IN. Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review. Int Endod J 2024; 57:1043-1058. [PMID: 38634795 DOI: 10.1111/iej.14071] [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: 10/19/2023] [Revised: 02/21/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis. OBJECTIVES This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis. METHODS The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist. RESULTS From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 105 to 106 in primary infections and from 103 to 104 in posttreatment infections. DISCUSSION Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis. CONCLUSIONS There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type. REGISTRATION PROSPERO CRD42021275886.
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Affiliation(s)
- José F Siqueira
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
| | - Warley O Silva
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
| | - Kaline Romeiro
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
| | - Luciana F Gominho
- Department of Restorative Dentistry, Federal University of Paraíba (UFPB), João Pessoa, PB, Brazil
| | - Flávio R F Alves
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
| | - Isabela N Rôças
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Rio de Janeiro, RJ, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, RJ, Brazil
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Li H, Li J, Hu J, Chen J, Zhou W. High-performing cross-dataset machine learning reveals robust microbiota alteration in secondary apical periodontitis. Front Cell Infect Microbiol 2024; 14:1393108. [PMID: 38975327 PMCID: PMC11224960 DOI: 10.3389/fcimb.2024.1393108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Multiple research groups have consistently underscored the intricate interplay between the microbiome and apical periodontitis. However, the presence of variability in experimental design and quantitative assessment have added a layer of complexity, making it challenging to comprehensively assess the relationship. Through an unbiased methodological refinement analysis, we re-analyzed 4 microbiota studies including 120 apical samples from infected teeth (with/without root canal treatment), healthy teeth, using meta-analysis and machine learning. With high-performing machine-learning models, we discover disease signatures of related species and enriched metabolic pathways, expanded understanding of apical periodontitis with potential therapeutic implications. Our approach employs uniform computational tools across datasets to leverage statistical power and define a reproducible signal potentially linked to the development of secondary apical periodontitis (SAP).
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Affiliation(s)
- Hao Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiehang Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiani Hu
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
- School of Chemistry Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jionglin Chen
- Research and Development Department, Beijing Xunzhu Biotechnology Co. Ltd., Beijing, China
| | - Wei Zhou
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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Huang C, Chu C, Peng Y, Zhang N, Yang Z, You J, Wei F. Correlations between gastrointestinal and oral microbiota in children with cerebral palsy and epilepsy. Front Pediatr 2022; 10:988601. [PMID: 36440329 PMCID: PMC9686843 DOI: 10.3389/fped.2022.988601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
We here studied the correlation between gut and oral microbiota in children with cerebral palsy and Epilepsy (CPE). We enrolled 27 children with this condition from the social welfare center of Longgang District, collected their oral plaque and stool samples, and analyzed their gut microbiota (GM) and oral microbiota (OM) through 16S rRNA gene sequencing. Taxonomical annotation revealed that the levels of Firmicutes and Bacteroides in the oral cavity were significantly lower in CPE children than in healthy children, whereas the abundance of Actinomycetes increased significantly in CPE children. In addition, Prevotella, Fusobacterium, and Neisseria were the top three abundant genera, representing 15.49%, 9.34%, and 7.68% of the OM and suggesting potential correlations with caries, periodontitis, and malnutrition. For the GM, Bifidobacterium, Bacteroides, and Prevotella were the top three abundant genera in CPE children and probably contributed to the development of chronic inflammation and malnutrition. Furthermore, the OM and GM correlated with each other closely, and the bacterial components of these microbiota in CPE children were remarkably different from those in healthy children, such as Bifidobacterium, Fusobacterium, Bacteroides, and Neisseria. Conclusively, dysbiotic OM can translocate to the intestinal tract and induce GM dysbiosis, suggesting the consistency between OM and GM variations. Altered oral and gut microbial structures have potential impacts on the occurrence of clinical diseases such as periodontitis, caries, and malnutrition.
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Affiliation(s)
- Congfu Huang
- Department of Pediatrics, Longgang District Maternity & Child Healthcare Hospital, Shenzhen, China
| | | | - Yuanping Peng
- The Outpatient Department, Longgang District Social Welfare Center, Shenzhen, China
| | - Nong Zhang
- Department of Pediatrics, Longgang District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Zhenyu Yang
- School of Statistics and Data Science, NanKai University, Tianjin, China
| | - Jia You
- Shenzhen Middle School, Shenzhen, China
| | - Fengxiang Wei
- Department of Pediatrics, Longgang District Maternity & Child Healthcare Hospital, Shenzhen, China
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The apical root canal system microbial communities determined by next-generation sequencing. Sci Rep 2020; 10:10932. [PMID: 32616783 PMCID: PMC7331743 DOI: 10.1038/s41598-020-67828-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/09/2020] [Indexed: 12/30/2022] Open
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.
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Dezhurko-Korol VA, Novozhilova NE, Makeeva IM, Arkhipova AY, Moisenovich MM, Akhmadishina LV, Lukashev AN, Semenov AM, Leontieva MR, Byakova SF. The influence of centrifugation and inoculation time on the number, distribution, and viability of intratubular bacteria and surface biofilm in deciduous and permanent bovine dentin. Arch Oral Biol 2020; 114:104716. [PMID: 32325265 DOI: 10.1016/j.archoralbio.2020.104716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/11/2020] [Accepted: 03/27/2020] [Indexed: 11/27/2022]
Abstract
The present study aimed to assess the influence of centrifugation and inoculation time on the number, distribution, and viability of intratubular bacteria and surface monospecies E. faecalis biofilm. MATERIALS AND METHODS Forty-four semicylindrical specimens cut from primary (n = 22) and permanent (n = 22) bovine teeth were randomly assigned to the experimental groups. Teeth of each type were inoculated with E. faecalis with and without centrifugation for 1 and 14 days. The number, localization, viability of bacteria and depth of their penetration were assessed with bacterial culturing of dentin shavings, scanning electron microscopy (SEM) and confocal laser electron microscopy (CLSM). Three-way ANOVA with post-hoc Tukey test were used to assess the influence of different experimental setups on dentin infection. RESULTS Severe dentin infection was observed in permanent and deciduous teeth after centrifugation and 1-day incubation: bacteria reached the full length of dentinal tubules and colony-forming units were too numerous to count. The volume of green fluorescence didn't differ significantly in permanent teeth compared with deciduous (p = 1.0). After 1-day stationary inoculation, small number of cultivable bacteria and few viable bacteria in dentinal tubules were found in both groups. After 14-day stationary inoculation, the dentin infection according to CLSM was deeper in deciduous teeth compared with permanent (p = 0.006 and p = 0.019 for centrifugation and stationary inoculation, respectively). CONCLUSION The most even and dense dentin infection was observed in primary and permanent bovine teeth after centrifugation and 1-day inoculation, and in deciduous teeth after 14-day stationary inoculation.
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Affiliation(s)
- Viktoria A Dezhurko-Korol
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
| | - Nina E Novozhilova
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia.
| | - Irina M Makeeva
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
| | - Anastasia Yu Arkhipova
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Mihail M Moisenovich
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Ludmila V Akhmadishina
- E.I. Martsinovsky Institute of Medical Parasitology and Tropical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), M. Pirogovskaya str., 20-1, 119435, Moscow, Russia
| | - Alexander N Lukashev
- E.I. Martsinovsky Institute of Medical Parasitology and Tropical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), M. Pirogovskaya str., 20-1, 119435, Moscow, Russia
| | - Alexander M Semenov
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Maria R Leontieva
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119991, Moscow, Russia
| | - Svetlana F Byakova
- Institute of Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Mojaiskii val str., 11, 121059б, Moscow, Russia
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Liu BY, Liu J, Zhang D, Yang ZL, Feng YP, Wang M. Effect of silver diammine fluoride on micro-ecology of plaque from extensive caries of deciduous teeth - in vitro study. BMC Oral Health 2020; 20:151. [PMID: 32448221 PMCID: PMC7247265 DOI: 10.1186/s12903-020-01141-3] [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: 03/02/2020] [Accepted: 05/17/2020] [Indexed: 11/19/2022] Open
Abstract
Background The mechanism of action of silver diammine fluoride (SDF) on plaque micro-ecology is seldom studied. This study investigated micro-ecological changes in dental plaque on extensive caries of deciduous teeth after topical SDF treatment. Methods Deciduous teeth with extensive caries freshly removed from school children were collected in clinic. Unstimulated saliva collection and initial plaque sampling were done before tooth extraction, then each caries was topically treated with 38% SDF in vitro. After intervention, each tooth was stored respectively in artificial saliva at 37 °C. Repeated plaque collections were done at 24 h and 1 week post-intervention. Post-intervention micro-ecological changes including microbial diversity, microbial metabolism function as well as species correlations were analyzed and compared after pyrosequencing of the DNA from the plaque sample using Illumina MiSeq platform. Results After SDF application, microbial diversity decreased (P > 0.05), although not statistically significant. Microbial community composition post-intervention was noticeably different from that of supragingival and pre-intervention plaque as well as saliva. At 1 week post-intervention, the relative content of Pseudomonas, Fusobacterium and Pseudoramibacter were higher than before, while most of the other bacteria were reduced, although the changes were not statistically significant (P > 0.05). The inter-microbial associations became more complex, much more positive associations among survived bacteria were observed than negative ones. COG function classification diagram showed carbohydrate transportation and metabolic functions in the plaque were significantly reduced at 24 h and 1 week post-intervention. Conclusions SDF has extensive antimicrobial effect on dental plaque, which may reduce carbohydrate metabolism in dental plaque and help promote new balance of the plaque flora.
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Affiliation(s)
- Bao Ying Liu
- The First Affiliated Hospital of Zhengzhou University (School and Hospital of Stomatology), No 1 Jianshe Road, Pingdingshan, 450001, Henan Province, China.
| | - Jin Liu
- The First Affiliated Hospital of Zhengzhou University (School and Hospital of Stomatology), No 1 Jianshe Road, Pingdingshan, 450001, Henan Province, China
| | - Di Zhang
- The First Affiliated Hospital of Zhengzhou University (School and Hospital of Stomatology), No 1 Jianshe Road, Pingdingshan, 450001, Henan Province, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhi Lei Yang
- The First Affiliated Hospital of Zhengzhou University (School and Hospital of Stomatology), No 1 Jianshe Road, Pingdingshan, 450001, Henan Province, China
| | - Ya Ping Feng
- The Second Affiliated Hospital of Pingdingshan College, Pingdingshan, Henan Province, China
| | - Meng Wang
- The Second Affiliated Hospital of Pingdingshan College, Pingdingshan, Henan Province, China
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Llena C, Almarche A, Mira A, López MA. Antimicrobial efficacy of the supernatant of Streptococcus dentisani against microorganisms implicated in root canal infections. J Oral Sci 2019; 61:184-194. [PMID: 30918216 DOI: 10.2334/josnusd.18-0239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The present study aimed to test the antimicrobial activity of Streptococcus dentisani (S. dentisani) supernatant against a collection of microorganisms implicated in dental root infections, and to analyze morphological changes induced in a selection of the tested microorganisms. A total of 22 microbial species were selected, and their growth was monitored by spectrophotometry in the presence and absence of the supernatant of S. dentisani at different assay concentrations (0.2×, 1×, 2×). The generation time and maximum growth rates were evaluated under every tested condition. Scanning electron microscope (SEM) images were obtained to assess the effect on the cell surface following incubation of the pathogens with the concentrated (2×) supernatant of S. dentisani. The supernatant of S. dentisani was found to exert effective inhibitory activity against most of the studied microorganisms implicated in dental root infections (20 out of 22). Total growth inhibition was observed in the case of Streptococcus oralis, Streptococcus sobrinus, Streptococcus salivarius, Prevotella intermedia, and Streptococcus mutans, while the rest of the microorganisms showed an increase in the generation time (between 30 min and 4 h). SEM images revealed structural changes in the membrane consistent with bacteriocin activity, although the effects were heterogeneous among the different species tested.
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Affiliation(s)
- Carmen Llena
- Department of Stomatology, University of Valencia
| | | | - Alejandro Mira
- The Foundation for the Promotion of Health and Biomedical Research (FISABIO)
| | - M Arantxa López
- The Foundation for the Promotion of Health and Biomedical Research (FISABIO)
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Qian W, Ma T, Ye M, Li Z, Liu Y, Hao P. Microbiota in the apical root canal system of tooth with apical periodontitis. BMC Genomics 2019; 20:189. [PMID: 30967114 PMCID: PMC6456935 DOI: 10.1186/s12864-019-5474-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral. Methods Four groups of specimens are considered, the apical part of root from diseased teeth with and without root canal treatment, and wisdom teeth extracted to avoid being impacted (tooth healthy control), as well as an additional healthy oral control from biofilm of the buccal mucosa. DNA was extracted from these specimens and the microbiome was examined through focusing on the V3-V4 hypervariable region of the 16S rRNA gene using sequencing on Illumina MiSeq platform. Composition and diversity of the bacterial community were tested for individual samples, and between-group comparisons were done through differential analysis to identify the significant changes. Results We observed reduced community richness and diversity in microbiota samples from diseased teeth compared to healthy controls. Through differential analysis between AP teeth and healthy teeth, we identified 49 OTUs significantly down-regulated as well as 40 up-regulated OTUs for AP. Conclusion This study provides a global view of the microbial community of the AP associated cohorts, and revealed that AP involved not only bacteria accumulated with a high abundance, but also those significantly reduced ones due to microbial infection. Electronic supplementary material The online version of this article (10.1186/s12864-019-5474-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenhao Qian
- Shanghai Xuhui District Dental Center, Shanghai, 200032, China
| | - Ting Ma
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mao Ye
- Shanghai Xuhui District Dental Center, Shanghai, 200032, China
| | - Zhiyao Li
- Shanghai Xuhui District Dental Center, Shanghai, 200032, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
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