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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections

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Author(s):
Nardello, Laura C. L. [1] ; Amado, Pamela P. P. [2] ; Franco, Diego C. [3] ; Cazares, Roberto X. R. [1] ; Nogales, Carlos G. [1] ; Mayer, Marcia P. A. [2] ; Karygianni, Lamprini [4] ; Thurnheer, Thomas [4] ; Pinheiro, Ericka T. [1, 4]
Total Authors: 9
Affiliation:
[1] Univ Sao Paulo, Sch Dent, Dept Dent, Av Prof Lineu Prestes 2227, BR-05508000 Sao Paulo, SP - Brazil
[2] Univ Sao Paulo, Inst Biomed Sci, Dept Microbiol, Sao Paulo - Brazil
[3] Jagiellonian Univ, Inst Environm Sci, Krakow - Poland
[4] Univ Zurich, Ctr Dent Med, Clin Conservat & Prevent Dent, Zurich - Switzerland
Total Affiliations: 4
Document type: Journal article
Source: JOURNAL OF ENDODONTICS; v. 46, n. 8, p. 1105-1112, AUG 2020.
Web of Science Citations: 0
Abstract

Introduction: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections. Methods: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P<.05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis. Results: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P<.05). The bacterial taxa Bacteroidales {[}G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA >= 1%) and active (rRNA/DNA >= 1). Conclusions: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections. (AU)

FAPESP's process: 19/12908-3 - Multispecies biofilm models to study new therapeutic strategies against secondary/persistent endodontic infections
Grantee:Ericka Tavares Pinheiro
Support Opportunities: Scholarships abroad - Research