Caries, DentalNCT07538089
Caries Removal Methods and Microbiome Changes
A study testing Non-selective caries removal and Selective caries removal in people with Caries, Dental, run by Nuh Naci Yazgan University at 1 site in Turkey (Türkiye).
Trial summary
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. Read more about this study
- Who is it for?
- Ages 18 to 40 yearsHealthy volunteers can take part
- Conditions the study is for
- Caries, Dental
- What is being tested?
- Non-selective caries removal and Selective caries removal
- Type of treatment
- Surgery or procedure
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 48 participants
- Where
- 1 siteTurkey (Türkiye)
- Study dates
- 26 Feb 2026to Aug 2026
- Phase
- Interventional
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 18 to 40 years
- All sexes
- Healthy volunteers accepted
- Adult
Who may be able to join
- 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
Who cannot join
- 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
Trial locations and contacts
1 site in 1 country.
Turkey (Türkiye)1 site
Nuh Naci Yazgan University Faculty of Dentistry
Kayseri, Kocasinan, 38170
About this study
Official title: 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.
Read the 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.
- Conditions
- Caries, Dental
- Being tested
- Non-selective caries removal, Selective caries removal
- Keywords
- Dental caries, Cavity microbiome
- Medical subject headings
- Dental Caries
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Non-selective caries removalProcedure or surgery
Also called Complete 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.
Selective caries removalProcedure or surgery
Also called Partial 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.
| Study group | Role | What they receive |
|---|---|---|
| Non-selective caries removal | Experimental | Complete removal of infected dentin using the non-selective caries removal approach. Receives: Procedure: Non-selective caries removal |
| Selective caries removal | Experimental | Selective removal of carious tissue with preservation of softened dentin near the pulp. Receives: Procedure: Selective caries removal |
What is being measured
The primary outcome is the main question the study is designed to answer.
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.
Measured: 3 months
Secondary outcomes (4)
Relative abundance of specific bacterial taxa
Measured using 16S rRNA sequencing to evaluate changes in key cariogenic and commensal bacteria after caries removal procedures.
Measured: 3 months
Alpha diversity of the oral microbiome
Assessed using diversity indices (e.g., Shannon index) to evaluate microbial richness and diversity within samples.
Measured: 3 months
Beta diversity of the oral microbiome
Evaluated to compare differences in microbial community composition between study groups.
Measured: 3 months
Presence of residual cariogenic bacteria
Assessment of remaining cariogenic microorganisms in the cavity after caries removal.
Measured: 3 months
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted20 Apr 2026
- Study start26 Feb 2026
- Primary completionMay 2026 (estimated)
- Study completionAug 2026 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Caries, DentalStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase N/A
- Primary purpose
- Basic science
- Allocation
- Randomised
- Intervention model
- Parallel groups
- Model description
- Group 1: Non-selective caries removal (complete excavation of infected dentin) Group 2: Selective caries removal (preservation of affected dentin near the pulp)
- Masking
- Single blind
- Who is masked
- Participant
- Enrolment
- 48 participants (actual)
Sponsor and investigators
- Lead sponsor
- Nuh Naci Yazgan University
- Sponsor type
- University, hospital or other
- Responsible party
- Principal investigator, Ozcan Karatas, Nuh Naci Yazgan University
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT07538089
- Sponsor's protocol ID
- 2024/1176
- Other IDs
- 2025-SA.KAP-6
- Status last verified
- Apr 2026
- First submitted
- 12 Apr 2026
- Last updated
- 20 Apr 2026
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- Undecided: 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.
Study at a glance
From the registry record, last updated by the sponsor on 20 Apr 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Microbiome Changes in Cavities Prepared With Different Caries Removal Methods
- ClinicalTrials.gov ID
- NCT07538089
- Acronym / sponsor ID
- 2024/1176
- Conditions
- Caries, Dental
- Keywords
- Dental caries, Cavity microbiome
- Study type
- Interventional
- Recruitment status
- Active, not recruiting
- Enrolment
- 48 participants (actual)
- Lead sponsor
- Nuh Naci Yazgan UniversityUniversity, hospital or other
- Study start
- 26 Feb 2026 (actual)
- Primary completion
- May 2026 (estimated)
- Study completion
- Aug 2026 (estimated)
- First posted
- 20 Apr 2026 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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.
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 design
- Primary purpose
- Basic science
- Allocation
- Randomised
- Intervention model
- Parallel groups
- Masking
- Single blind (participant)
- Number of arms
- 2
- Model description
- Group 1: Non-selective caries removal (complete excavation of infected dentin) Group 2: Selective caries removal (preservation of affected dentin near the pulp)
| Arm | Type | Receives |
|---|---|---|
| Non-selective caries removal | Experimental | Procedure: Non-selective caries removalComplete removal of infected dentin using the non-selective caries removal approach. |
| Selective caries removal | Experimental | Procedure: Selective caries removalSelective removal of carious tissue with preservation of softened dentin near the pulp. |
Who may qualify
- Ages
- 18 to 40 years
- Sex
- All
- Healthy volunteers
- Accepted
- Age groups
- Adult
Key inclusion criteria (6 listed)
- 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
Key exclusion criteria (6 listed)
- 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
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Non-selective caries removalAlso: Complete caries removalNon-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. | Procedure or surgery | Non-selective caries removal |
| Selective caries removalAlso: Partial caries removalSelective 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. | Procedure or surgery | Selective caries removal |
Primary outcome
Microbiome Changes
Time frame: 3 months
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.
4 secondary outcomes
Relative abundance of specific bacterial taxa
Time frame: 3 months
Alpha diversity of the oral microbiome
Time frame: 3 months
Beta diversity of the oral microbiome
Time frame: 3 months
Presence of residual cariogenic bacteria
Time frame: 3 months
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 20 Apr 2026.
- Individual participant dataSharing planned: Undecided. 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.
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
The record lists no contact. Use the official record to reach the sponsor.
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing Non-selective caries removal and Selective caries removal in people with Caries, Dental, run by Nuh Naci Yazgan University at 1 site in Turkey (Türkiye).
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 6 inclusion and 6 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: under way, not looking for participants, as of the sponsor's last update on 20 Apr 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Turkey (Türkiye). Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Microbiome Changes (time frame: 3 months). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 20 Apr 2026.