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Ev LD, Poloni JDF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, Do T, Maltz M, Parolo CCF. Hub genes and pathways related to caries-free dental biofilm: clinical metatranscriptomic study. Clin Oral Investig 2023; 27:7725-7735. [PMID: 37924358 DOI: 10.1007/s00784-023-05363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
OBJECTIVE This study aimed to evaluate the microbial functional profile of biofilms related to caries-free (CF, n = 6) and caries-arrested (CI, n = 3) compared to caries-active (CA, n = 5) individuals. MATERIALS AND METHODS A metatranscriptomic was performed in supragingival biofilm from different clinical conditions related to caries or health. Total RNA was extracted and cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data (SortMeRNA) were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2) and weighted gene co-expression network analysis (WCGNA) to explore and identify gene modules related to these clinical conditions. RESULTS A total of 5303 genes were found in the metatranscriptomic analysis. A co-expression network identified the most relevant modules strongly related to specific caries status. Correlation coefficients were calculated between the eigengene modules and the clinical conditions (CA, CI, and CF) discriminating multiple modules. CA and CI showed weak correlation coefficient strength across the modules, while the CF condition presented a very strong positive correlation coefficient (r = 0.9, p value = 4 × 10-9). Pearson's test was applied to further analyze the module membership and gene significance in CF conditions, and the most relevant were HSPA1s-K03283, Epr- K13277, and SLC1A-K05613. Gene Ontology (GO) shows important bioprocesses, such as two-component system, fructose and mannose metabolism, pentose and glucuronate interconversions, and flagellar assembly (p-adjust < 0.05). The ability to use different carbohydrates, integrate multiple signals, swarm, and bacteriocin production are significant metabolic advantages in the oral environment related to CF. CONCLUSIONS A distinct functional health profile could be found in CF, where co-occurring genes can act in different pathways at the same time. Genes HSPA1s, Epr, and SLC1A may be appointed as potential biomarkers for caries-free biofilms. CLINICAL RELEVANCE Potential biomarkers for caries-free biofilms could contribute to the knowledge of caries prevention and control.
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Affiliation(s)
- Laís Daniela Ev
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Joice de Faria Poloni
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, National Institute of Science and Technology - Forensic Science, Porto Alegre, Brazil
| | - Nailê Damé-Teixeira
- Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, DF, Brazil
| | - Rodrigo Alex Arthur
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daniela Jorge Corralo
- Department of Dentistry, School of Dentistry, Passo Fundo University, Passo Fundo, RS, Brazil
| | - Sandra Liana Henz
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Thuy Do
- Division of Oral Biology, School of Dentistry, Faculty of Medicine & Health, University of Leeds, Leeds, UK
| | - Marisa Maltz
- Department of Preventive and Social Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Ev LD, Poloni JF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, DO T, Maltz M, Parolo CCF. Biofilm dysbiosis and caries activity: a surface or an individual issue? J Appl Oral Sci 2023; 31:e20230214. [PMID: 37970886 PMCID: PMC10697669 DOI: 10.1590/1678-7757-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVE This study aimed to analyze the functional profile of supragingival biofilm from sound (CAs), active (CAa), and inactive (CAi) enamel caries lesions from caries-active individuals to provide insights into the diversity of biological processes regarding biofilm dysbiosis. METHODOLOGY A metatranscriptome analysis was performed in biofilm samples collected from five caries-active individuals. Total RNA was extracted, and the microbial cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2). RESULTS Bioinformatics analysis of mRNAs revealed a similar functional profile related to all analyzed conditions (CAa, CAi, and CAs). However, active and inactive surfaces share up-regulated genes (gtsA; qrtT; tqsA; pimB; EPHX1) related to virulence traits that were not overrepresented in sound surfaces. From a functional perspective, what matters most is the individual carious status rather than the surface condition. Therefore, pooling samples from various sites can be carried out using naturally developed oral biofilms but should preferably include carious surfaces. CONCLUSION Metatranscriptome data from subjects with caries activity have shown that biofilms from sound, arrested, and active lesions are similar in composition and function.
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Affiliation(s)
- Laís Daniela Ev
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Joice Faria Poloni
- Instituto Nacional de Ciência e Tecnologia - Ciências Forense, Pontifica Universidade Católica do Rio Grande do Sul, Escola de Ciências da Saúde e da Vida, Porto Alegre, Brasil
| | - Nailê Damé-Teixeira
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, DF, Brasil
| | - Rodrigo Alex Arthur
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Daniela Jorge Corralo
- Universidade de Passo Fundo, Escola de Odontologia, Departamento de Odontologia, RS, Passo Fundo, Brasil
| | - Sandra Liana Henz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Thuy DO
- University of Leeds, School of Dentistry, Division of Oral Biology, Leeds, UK
| | - Marisa Maltz
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
| | - Clarissa Cavalcanti Fatturi Parolo
- Universidade Federal do Rio Grande do Sul, Faculdade de Odontologia, Departamento de Odontologia Preventiva e Social, Porto Alegre, RS, Brasil
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Corralo DJ, Ev LD, Damé-Teixeira N, Maltz M, Arthur RA, Do T, Fatturi Parolo CC. Functional Active Microbiome in Supragingival Biofilms in Health and Caries. Caries Res 2021; 55:603-616. [PMID: 34380135 DOI: 10.1159/000518963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Daniela Jorge Corralo
- PhD by Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Passo Fundo University (UPF), Passo Fundo, Brazil
| | - Laís Daniela Ev
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Nailê Damé-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasília, Federal District, Brasília, Brazil
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Marisa Maltz
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rodrigo Alex Arthur
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Thuy Do
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Clarissa Cavalcanti Fatturi Parolo
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Damé-Teixeira N, Ev LD, Bitello-Firmino L, Soares VK, Dalalba RS, Rup AG, Maltz M, Parolo CCF. Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing. Arch Oral Biol 2020; 121:104988. [PMID: 33242691 DOI: 10.1016/j.archoralbio.2020.104988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To characterize lactobacilli isolated from residual carious dentin after selective caries removal (SCR), by observing the changes detected in their prevalence, diversity, and cariogenic potential after starvation stress caused by cavity sealing (CS). DESIGN Lactobacilli were cultured from carious dentin lesions (n = 16 patients) treated in a clinical trial, three months before and after CS. Presumptive lactobacilli were selected, isolated, and analyzed by Gram staining. Housekeeping gene sequences were used to identify the species (groEL, rpoA, pheS, and 16S rRNA). RESULTS N = 86 Lactobacillus spp. (n = 41 before and n = 45 after sealing) were genotyped by AP-PCR and analyzed for their cariogenic potential (acid production and acid tolerance). The proportion of lactobacilli to the total anaerobic counts was high, and a significant decrease was observed after sealing (median before sealing = 78.9; 25th-75th = 60.25-97.35; median after sealing = 0.00; 25th-75th = 0.00-77.08; p = 0.001). L. paracasei was the most prevalent species of lactobacilli in carious dentin (p = 0.02). L. rhamnosus prevalence increased to a proportion similar to L. paracasei after CS (p = 0.001). A total of 28 and 14 different genotypes were found before and after CS, respectively. There was no difference between the L. paracasei and the L. rhamnosus isolated from carious dentin, neither regarding acid production nor acid tolerance. CONCLUSIONS Although there was a significant reduction in lactobacilli in the residual carious dentin after SCR, some strains were capable of surviving after three months of CS. However, the sealed available nutrients are low and not sufficient for caries progression. Also, we believe that a longer follow up period may eliminate all the residual lactobacilli. L. paracasei prevailed in carious dentin in a proportion similar to L. rhamnosus in the sealed dentin. Characterization of lactobacilli after SCR and sealing may help the understanding the importance of genotyping of lactobacilli in carious microbiota.
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Affiliation(s)
- Nailê Damé-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Federal District, Brazil.
| | - Laís Daniela Ev
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana Bitello-Firmino
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Vanessa Kern Soares
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Raquel Soares Dalalba
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ariel Goulart Rup
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marisa Maltz
- Department of Social and Preventive Dentistry, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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Ev LD, Damé-Teixeira N, DO T, Maltz M, Parolo CCF. The role of Candida albicans in root caries biofilms: an RNA-seq analysis. J Appl Oral Sci 2020; 28:e20190578. [PMID: 32348446 PMCID: PMC7185980 DOI: 10.1590/1678-7757-2019-0578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/19/2020] [Indexed: 11/30/2022] Open
Abstract
Objective This study sought to analyze the gene expression of Candida albicans in sound root surface and root caries lesions, exploring its role in root caries pathogenesis. Methodology The differential gene expression of C. albicans and the specific genes related to cariogenic traits were studied in association with samples of biofilm collected from exposed sound root surface (SRS, n=10) and from biofilm and carious dentin of active root carious lesions (RC, n=9). The total microbial RNA was extracted, and the cDNA libraries were prepared and sequenced on the Illumina Hi-Seq2500. Unique reads were mapped to 163 oral microbial reference genomes including two chromosomes of C. albicans SC5314 (14,217 genes). The putative presence of C. albicans was estimated (sum of reads/total number of genes≥1) in each sample. Count data were normalized (using the DESeq method package) to analyze differential gene expression (using the DESeq2R package) applying the Benjamini-Hochberg correction (FDR<0.05). Results Two genes (CaO19.610, FDR=0.009; CaO19.2506, FDR=0.018) were up-regulated on SRS, and their functions are related to biofilm formation. Seven genes ( UTP20 , FDR=0.018; ITR1 , FDR=0.036; DHN6 , FDR=0.046; CaO19.7197 , FDR=0.046; CaO19.7838 , FDR=0.046; STT4 , FDR=0.046; GUT1 , FDR=0.046) were up-regulated on RC and their functions are related to metabolic activity, sugar transport, stress tolerance, invasion and pH regulation. The use of alternative carbon sources, including lactate, and the ability to form hypha may be a unique trait of C. albicans influencing biofilm virulence. Conclusions C. albicans is metabolically active in SRS and RC biofilm, with different roles in health and disease.
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Affiliation(s)
- Laís Daniela Ev
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Nailê Damé-Teixeira
- Departamento de Odontologia, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Distrito Federal, Brasil
| | - Thuy DO
- School of Dentistry, Faculty of Medicine & Health, University of Leeds, Leeds, United Kingdom
| | - Marisa Maltz
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Clarissa Cavalcanti Fatturi Parolo
- Departamento de Odontologia Preventiva e Social, Faculdade de Odontologia, Universidade de Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
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