Caries Removal Methods and Microbiome Changes

Microbiome Changes in Cavities Prepared With Different Caries Removal Methods

Dental caries management approaches may influence not only tissue removal but also the microbial composition within the cavity. However, clinical evidence on how different caries removal methods affect the oral microbiome remains limited.

This study aims to evaluate the effects of selective and non-selective caries removal methods on the diversity and composition of the oral microbiome using 16S rRNA gene sequencing. The findings are expected to help identify biologically compatible treatment approaches that effectively reduce pathogenic microorganisms.

Study Overview

• Status: Active, not recruiting
• Conditions: Caries, Dental
• Intervention / Treatment: Procedure: Non-selective caries removal; Procedure: Selective caries removal

Detailed Description

Dental caries is a highly prevalent chronic disease and a major cause of tooth loss, arising from a disruption in the dynamic balance between demineralization and remineralization processes. Acidogenic microorganisms within the oral biofilm drive mineral loss in enamel and dentin, leading to lesion progression.

Beyond mechanical debridement, the method of caries removal plays a critical role in modulating the residual microbial environment and influencing the biological response of the pulp-dentin complex. Conventional (non-selective) caries removal aims to eliminate all infected dentin; however, this approach may result in excessive tissue removal, including dentin with remineralization potential, and may increase the risk of pulpal stress or exposure.

In contrast, minimally invasive dentistry emphasizes the preservation of tooth structure and the maintenance of pulp vitality. Selective caries removal has emerged as a biologically oriented strategy in which caries is completely removed at the periphery of the cavity while softened dentin adjacent to the pulp is preserved. This approach is designed to reduce the risk of pulp exposure and to support the reparative and remineralization capacity of the remaining dentin.

Despite increasing clinical adoption, the microbiological consequences of different caries removal strategies remain incompletely understood. Traditional culture-based methods provide limited insight into the complexity of the oral microbiota, as a substantial proportion of oral microorganisms cannot be cultivated under standard laboratory conditions.

The advent of 16S rRNA gene sequencing has enabled high-resolution, culture-independent characterization of microbial communities, offering a comprehensive view of microbial diversity and composition within carious lesions. This approach provides an opportunity to better understand how clinical interventions shape the oral microbiome.

However, clinical evidence evaluating the impact of selective versus non-selective caries removal on the cavity microbiome using 16S rRNA sequencing remains scarce. Given that the quantity and quality of residual dentin may influence both mechanical properties and microbial persistence, elucidating these effects is critical for advancing biologically driven treatment strategies.

The aim of this study is to compare the effects of selective and non-selective caries removal methods on the diversity and composition of the oral microbiome using 16S rRNA gene sequencing. The findings are expected to provide insights into the microbiological outcomes of minimally invasive approaches and to inform the development of optimized clinical protocols that balance dentin preservation with effective microbial control.

• Study Type: Interventional
• Enrollment (Actual): 48
• Phase: Not Applicable

Contacts and Locations

Study Locations

• Turkey (Türkiye)
  • Kocasinan
    • Kayseri, Kocasinan, Turkey (Türkiye), 38170
      • Nuh Naci Yazgan University Faculty of Dentistry

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult
• Accepts Healthy Volunteers: Yes

Description

Inclusion Criteria:

• Permanent molar or premolar teeth with carious lesions located on the occlusal surface and extending no deeper than the middle third of dentin
• Individuals with good oral hygiene
• Absence of clinical signs or symptoms of periapical pathology
• Teeth in occlusion with the opposing dentition
• Individuals aged between18-40 years
• Individuals who provide written informed consent

Exclusion Criteria:

• Teeth with pulpal exposure or irreversible pulpitis
• Presence of periapical pathology
• Poor oral hygiene
• Patients with systemic conditions affecting oral health or healing
• Use of antibiotics within the last 3 months
• Pregnant or lactating individuals

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Basic Science
• Allocation: Randomized
• Interventional Model: Parallel Assignment
• Masking: Single

Number of Arms

2

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Experimental: Non-selective caries removal; Complete removal of infected dentin using the non-selective caries removal approach.	Procedure: Non-selective caries removal; Non-selective caries removal involves the complete excavation of infected dentin using conventional rotary instruments. Both infected and affected dentin are removed until hard dentin is reached, aiming to eliminate all carious tissue.; Other Names: Complete caries removal
Experimental: Selective caries removal; Selective removal of carious tissue with preservation of softened dentin near the pulp.	Procedure: Selective caries removal; Selective caries removal involves complete caries removal at the cavity margins while preserving softened dentin near the pulp to reduce the risk of pulp exposure and maintain tooth vitality.; Other Names: Partial caries removal

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Microbiome Changes	In all groups, dentin samples will be taken from the affected dentin at the base of the cavity after caries removal using two sterile, size 6 round steel burs moistened with saline solution for microbial analysis. The burs will be placed in 5 ml sterile vials and stored at -80 0C until the analyses are performed. The prepared cavities will be completed with routine and standard treatment protocols. Following the finishing and polishing procedures, occlusion will be checked. The samples collected during the research process will be delivered to the A&D Genetic Diseases Evaluation Centre (Ankara, Turkey) where DNA isolation and sequence analysis will be performed together with molecular biologists. In the method, following the extraction of total genomic DNA from clinical samples, broad-range 16S rRNA PCR will be performed and MicroSeq 500 16S rRNA Sequencing kit will be used for sequence analysis.	3 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Relative abundance of specific bacterial taxa	Measured using 16S rRNA sequencing to evaluate changes in key cariogenic and commensal bacteria after caries removal procedures.	3 months
Alpha diversity of the oral microbiome	Assessed using diversity indices (e.g., Shannon index) to evaluate microbial richness and diversity within samples.	3 months
Beta diversity of the oral microbiome	Evaluated to compare differences in microbial community composition between study groups.	3 months
Presence of residual cariogenic bacteria	Assessment of remaining cariogenic microorganisms in the cavity after caries removal.	3 months

Collaborators and Investigators

• Sponsor: Nuh Naci Yazgan University

Study record dates

Study Major Dates

• Study Start (Actual): February 26, 2026
• Primary Completion (Estimated): May 1, 2026
• Study Completion (Estimated): August 1, 2026

Study Registration Dates

• First Submitted: April 12, 2026
• First Submitted That Met QC Criteria: April 12, 2026
• First Posted (Actual): April 20, 2026

Study Record Updates

• Last Update Posted (Actual): April 20, 2026
• Last Update Submitted That Met QC Criteria: April 12, 2026
• Last Verified: April 1, 2026

More Information

Terms related to this study

• Keywords: Dental caries; Cavity microbiome
• Additional Relevant MeSH Terms: Stomatognathic Diseases; Tooth Diseases; Tooth Demineralization; Dental Caries
• Other Study ID Numbers: 2024/1176; 2025-SA.KAP-6 (Other Grant/Funding Number: Nuh Naci Yazgan University)

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED
• IPD Plan Description: The plan to share individual participant data has not yet been determined. Data sharing will be considered in the future in accordance with ethical guidelines, institutional policies, and participant confidentiality.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No