The goal of this clinical trial is to learn how the bacterial profile in infected root canals changes during different phases of routine root canal treatment in adults with chronic apical abscess. The main questions it aims to answer are:

• How does the root canal bacterial profile change before and after irrigation with 5.25 percent sodium hypochlorite or 3 percent sodium hypochlorite?
• How does the bacterial profile change after calcium hydroxide medicament is placed in the root canal?

Participants will:

• Receive standard root canal treatment with one of two irrigation regimens (5.25 percent or 3 percent sodium hypochlorite, plus EDTA),
• Have root canal samples taken three times (before any treatment, after irrigation, and after calcium hydroxide medicament), and
• Have the bacteria in these samples analyzed using 16S rRNA PCR and DNA sequencing.

Chronic apical abscess is associated with complex multispecies biofilms in the root canal that can differ between populations and are not fully characterized by conventional culture methods. This study focuses on adult patients with necrotic molar teeth and chronic apical abscess treated at the Dental and Oral Hospital, Faculty of Dentistry, Hasanuddin University. The main objective is to describe how the root canal bacterial community profile changes during different phases of routine root canal treatment using 16S rRNA PCR and sequence analysis.

The study uses a descriptive and analytic repeated-measures design. At least 24 adult outpatients with necrotic pulp and chronic apical abscess who meet the inclusion and exclusion criteria will be recruited and provide written informed consent. After rubber dam isolation, access cavity preparation, and working length determination, the first root canal sample (S1) is collected from the distal canal using a sterile Hedström file and transferred into a tube containing DNA preservative solution. Mechanical preparation is then performed with rotary instruments. Patients are randomly assigned by clinic staff, who are blinded to the investigator, to one of two irrigation regimens: 5.25 percent sodium hypochlorite or 3 percent sodium hypochlorite, each followed by sterile distilled water, 17 percent EDTA, and a final rinse with sterile distilled water. A second sample (S2) is collected from the same canal after irrigation. Calcium hydroxide intracanal medicament is then placed and the tooth is temporized.

After approximately two weeks, the temporary restoration and calcium hydroxide are removed, and a third sample (S3) is collected from the same canal using a sterile Hedström file. All samples are stored in DNA preservative solution and analyzed by 16S rRNA PCR followed by DNA sequencing to characterize the bacterial community composition and diversity. The study will compare bacterial taxa and community profiles at S1, S2, and S3 and between the two sodium hypochlorite concentrations in order to explore how root canal irrigation and calcium hydroxide medicament are associated with changes in the bacterial community.

Inclusion Criteria:

• Adult aged between 18 and 75 years.
• Physically and mentally able to undergo treatment
• Have not used antibiotics within 1 week before treatment.
• Permanent molar teeth showing clinical and radiographic signs of chronic apical abscess and considered restorable.
• Willing to participate in the study and able to provide written informed consent after receiving an explanation of the study.

Exclusion Criteria:

• Systemic conditions that require antibiotic prophylaxis for routine dental treatment or other significant systemic disease.
• Pregnant or breastfeeding women.
• Participants with cognitive impairment.
• Teeth with advanced mobility (greater than grade 2).
• Teeth with periodontal pockets deeper than 4 mm.
• Teeth with radiographic signs of root resorption.
• Teeth with calcification or obliteration of the root canal.
• Teeth with root fracture or that fracture during treatment.
• Teeth with open apices.

Individual participant data will not be shared because of privacy considerations and institutional and ethics committee policies that restrict sharing of identifiable clinical data outside the study team.