Taxonomic abundance in primary and secondary root canal infections

Abstract Aim To evaluate the root canal microbiome composition in cases of primary and secondary apical periodontitis. Methodology Thirty‐nine samples from patients with primary root canal infections obtained before root canal treatment, and 40 samples obtained during root‐end resection procedures from previously filled cases with apical periodontitis were evaluated using 16S rRNA next‐generation sequencing analysis (NGS). Demographic and clinical factors included age, sex, infection type, percussion sensitivity, and presence of pain. Differences in abundances of genera were evaluated using Kruskal‐Wallis test. Alpha and beta diversity indices were calculated using mothur. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray–Curtis dissimilarity was used to measure beta diversity. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bonferroni correction for multiple comparisons. Results Significantly fewer operational taxonomic units values were observed from samples from secondary infections (p < .0001). While no significant differences were observed in the Chao 1 index between primary and secondary infections, the Shannon alpha diversity was significantly lower in secondary relative to primary infections (p = .008). Among samples, sex, age (adult vs. older adult), percussion sensitivity, and presence of pain all showed no significant effects on community composition via an analysis of similarity (ANOSIM). However, community composition was significantly different depending on whether the sample was from a primary or secondary infection (R = .051, p = .03). Nine microbial genera comprised the predominant taxa observed among samples (>3.3%) and included Parvimonas, Fusobacterium, Campylobacter, Arachnia, Eubacterium, Prevotella, Peptostreptococcus, Fretibacterirum, and Pseudoramibacter. Significantly greater relative abundances of Prevotella, Peptostreptococcus, Veillonella, Lactucaseibacillus, and Dialister were observed in primary infections. Conclusions Primary endodontic infections are more diverse than secondary infections. The microbial composition is not associated with the clinical manifestations of apical periodontitis.

[1]  J. Merritt,et al.  Development of the First Tractable Genetic System for Parvimonas micra, a Ubiquitous Pathobiont in Human Dysbiotic Disease , 2022, bioRxiv.

[2]  Yong Nie,et al.  Microbial Communities in the Extraradicular and Intraradicular Infections Associated With Persistent Apical Periodontitis , 2022, Frontiers in Cellular and Infection Microbiology.

[3]  T. M. Duque,et al.  Prevalence of red and orange microbial complexes in endodontic-periodontal lesions: a systematic review and meta-analysis , 2021, Clinical Oral Investigations.

[4]  D. Manoil,et al.  Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges , 2021, Frontiers in Oral Health.

[5]  T. Janatova,et al.  The Oral Microbiome in Periodontal Health , 2021, Frontiers in Cellular and Infection Microbiology.

[6]  C. Seneviratne,et al.  Role of the oral microbiome, metabolic pathways, and novel diagnostic tools in intra-oral halitosis: a comprehensive update , 2021, Critical reviews in microbiology.

[7]  C. Michelon,et al.  The global prevalence of apical periodontitis: a systematic review and meta-analysis. , 2020, International endodontic journal.

[8]  L. E. Chávez de Paz,et al.  New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth , 2020, Journal of clinical medicine.

[9]  Warley Luciano Fonseca Tavares,et al.  The apical root canal system microbial communities determined by next-generation sequencing , 2020, Scientific Reports.

[10]  M. Feres,et al.  Do patients with aggressive and chronic periodontitis exhibit specific differences in the subgingival microbial composition? A systematic review. , 2020, Journal of periodontology.

[11]  V. Crincoli,et al.  Prevalence of the Genus Propionibacterium in Primary and Persistent Endodontic Lesions: A Systematic Review , 2020, Journal of clinical medicine.

[12]  E. Kokubu,et al.  Synergistic biofilm formation by Parvimonas micra and Fusobacterium nucleatum. , 2020, Anaerobe.

[13]  A. Valm.  The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease. , 2019, Journal of molecular biology.

[14]  J. Schrenzel,et al.  Root Microbiota in Primary and Secondary Apical Periodontitis , 2018, Front. Microbiol..

[15]  A. Gonçalves,et al.  Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing , 2018, International endodontic journal.

[16]  I. N. Rôças,et al.  Microbial Analysis of Endodontic Infections in Root‐filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing , 2018, Journal of endodontics.

[17]  R. Isaacson,et al.  Deciphering Diversity Indices for a Better Understanding of Microbial Communities. , 2017, Journal of microbiology and biotechnology.

[18]  C. Keskin,et al.  Pyrosequencing Analysis of Cryogenically Ground Samples from Primary and Secondary/Persistent Endodontic Infections , 2017, Journal of endodontics.

[19]  I. N. Rôças,et al.  Microbiome in the Apical Root Canal System of Teeth with Post-Treatment Apical Periodontitis , 2016, PloS one.

[20]  Dan Knights,et al.  Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies , 2016, Nature Biotechnology.

[21]  D. Harris,et al.  Frequency, impact, and predictors of persistent pain after root canal treatment: a national dental PBRN study , 2016, Pain.

[22]  Dongseok Choi,et al.  Oral microbiota species in acute apical endodontic abscesses , 2016, Journal of oral microbiology.

[23]  Qiang Feng,et al.  Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer , 2015, Gut.

[24]  K. Divaris,et al.  Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing. , 2015, Journal of endodontics.

[25]  M. Costalonga,et al.  The oral microbiome and the immunobiology of periodontal disease and caries. , 2014, Immunology letters.

[26]  A. Al-Ahmad,et al.  Comparison of the Bacterial Composition and Structure in Symptomatic and Asymptomatic Endodontic Infections Associated with Root-Filled Teeth Using Pyrosequencing , 2013, PloS one.

[27]  Joonhong Park,et al.  Microbial analysis in primary and persistent endodontic infections by using pyrosequencing. , 2013, Journal of endodontics.

[28]  Erik Aronesty,et al.  Comparison of Sequencing Utility Programs , 2013 .

[29]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[30]  David J. Edwards,et al.  Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data , 2012, PloS one.

[31]  Adam M. Phillippy,et al.  Interactive metagenomic visualization in a Web browser , 2011, BMC Bioinformatics.

[32]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[33]  Patrick D. Schloss,et al.  Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis , 2011, Applied and Environmental Microbiology.

[34]  Susan M. Huse,et al.  Ironing out the wrinkles in the rare biosphere through improved OTU clustering , 2010, Environmental microbiology.

[35]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[36]  I. N. Rôças,et al.  The Microbiota of Acute Apical Abscesses , 2009, Journal of dental research.

[37]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[38]  Susan M. Huse,et al.  Pyrosequencing analysis of the Oral Microflora of healthy adults , 2008, Journal of dental research.

[39]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[40]  T. Karasawa,et al.  The microbial synergy of Peptostreptococcus micros and Prevotella intermedia in a murine abscess model. , 2004, Oral microbiology and immunology.

[41]  José F Siqueira,et al.  Association of Enterococcus faecalis with different forms of periradicular diseases. , 2004, Journal of endodontics.

[42]  J. Siqueira.  Periapical Actinomycosis and infection with Propionibacterium Propionicum , 2003 .

[43]  L. E. Chávez de Paz,et al.  Bacteria recovered from teeth with apical periodontitis after antimicrobial endodontic treatment. , 2003, International endodontic journal.

[44]  Marti J. Anderson,et al.  CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY , 2003 .

[45]  B. Gomes,et al.  Microorganisms from canals of root-filled teeth with periapical lesions. , 2003, International endodontic journal.

[46]  Qiang Zhu,et al.  PCR-Based Identification of Bacteria Associated with Endodontic Infections , 2002, Journal of Clinical Microbiology.

[47]  C. Reit,et al.  Microbiological status of root-filled teeth with apical periodontitis. , 1998, International endodontic journal.

[48]  U Sjögren,et al.  Microbiologic analysis of teeth with failed endodontic treatment and the outcome of conservative re-treatment. , 1998, Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics.

[49]  J. de Graaff,et al.  Pathogenicity of Peptostreptococcus micros morphotypes and Prevotella species in pure and mixed culture. , 1998, Journal of medical microbiology.

[50]  K. R. Clarke,et al.  Non‐parametric multivariate analyses of changes in community structure , 1993 .

[51]  M. B. Edlund,et al.  Peptostreptococcus micros has a uniquely high capacity to form hydrogen sulfide from glutathione. , 1993, Oral microbiology and immunology.

[52]  E. Johansson,et al.  Prevalence of black-pigmented bacteroides species in root canal infections. , 1989, Journal of endodontics.

[53]  K. Kahnberg,et al.  Survival of Arachnia propionica in periapical tissue. , 1988, International endodontic journal.

[54]  R. Happonen.  Periapical actinomycosis: a follow-up study of 16 surgically treated cases. , 1986, Endodontics & dental traumatology.

[55]  H. Shah,et al.  Black-pigmented Bacteroides spp. in human apical periodontitis , 1986, Infection and immunity.

[56]  L. Pelliniemi,et al.  Immunocytochemical demonstration of Actinomyces species and Arachnia propionica in periapical infections. , 1985, Journal of oral pathology.

[57]  J. Mycielski.  What is a mathematical theory , 1985 .

[58]  A. Chao.  Nonparametric estimation of the number of classes in a population , 1984 .

[59]  J. T. Curtis,et al.  An Ordination of the Upland Forest Communities of Southern Wisconsin , 1957 .