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.

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.

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

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.