Microbial assays in endodontic infections: A comprehensive narrative review of culture and molecular diagnostic protocols

Abstract

Endodontic infections are polymicrobial in nature, predominantly composed of anaerobic bacteria that colonize the root canal system and form biofilms resistant to conventional therapy. Understanding the microbial etiology of endodontic disease is crucial for successful treatment outcomes. Over the past three decades, significant advances have been made in characterizing endodontic microbiota through both conventional culture techniques and modern molecular methodologies. This narrative review synthesizes current knowledge regarding microbial assay protocols in endodontics, examining the purpose and clinical significance of endodontic treatment in eliminating infection, the diversity of common endodontic microorganisms and their biofilm formation, the importance and applications of microbial assays, and the classification of diagnostic approaches including both culture-dependent and culture-independent molecular methods. We review sample collection methodologies, present a comprehensive comparison of culture versus molecular techniques, and discuss the clinical applications of these assays in improving treatment outcomes. While culture-based techniques remain valuable for assessing bacterial viability and antibiotic susceptibility, molecular methods provide enhanced sensitivity and detect uncultivable species previously unrecognized in endodontic infections. This review emphasizes that neither approach is mutually exclusive; rather, complementary use of both methodologies provides the most comprehensive understanding of endodontic microbiology and guides clinical decision-making for improved patient outcomes.