Oral microbiome profiling of primary oral candidiasis during infection and post-antifungal therapy

OBJECTIVES: Microbial dysbiosis that facilitates Candida proliferation in the oral cavity is a significant factor associated with oral candidiasis. This study aimed to gain insights into microbial dynamics of primary oral candidiasis during infection and following antifungal therapy to enhance our understanding of disease pathogenesis and treatment efficacy. MATERIALS AND METHODS: Oral rinse samples were collected from 16 patients with primary oral candidiasis, seven of whom returned for follow-up after antifungal treatment, and from seven healthy controls. Microbiome profiling was performed using 16S rRNA gene sequencing (V3-V4 region), followed by microbial diversity and taxonomic analyses. RESULTS: Twelve bacterial phyla and 138 genera were identified across all samples. Alpha and beta diversity analyses showed no significant differences in microbial richness or overall community structure across both infection and treatment conditions, suggesting a resilient oral microbiome. Compared to controls, oral microbiome of the patients showed a significantly higher abundance of Firmicutes and Campylobacterota, along with a lower abundance of Bacteroidota. At the genus level, Campylobacter, Staphylococcus, and lactobacilli (Lacticaseibacillus, Ligilactobacillus, and Limosilactobacillus) were present at higher abundances during oral candidiasis, while Neisseria, Prevotella, and Alloprevotella were less abundant. Following two weeks of antifungal therapy, alterations in microbial community composition and diversity were observed relative to the control group, suggesting incomplete microbiota restoration. CONCLUSION: Microbiome analysis revealed dysbiosis with significant taxa changes during primary oral candidiasis. Clinical resolution of oral candidiasis did not correspond well with microbiota restoration, suggesting dysbiosis may persist beyond fungal clearance and contribute to delayed ecological recovery and oral homeostasis. CLINICAL RELEVANCE: This study highlights the microbial shift during primary oral candidiasis and post-antifungal treatment. Despite clinical resolution with antifungal therapy, oral microbiome of patients with primary oral candidiasis continues to exhibit residual shifts in composition, underscoring the needs for microbiota-targeted intervention to prevent recurrence and maintain oral health. While our results provide preliminary insights into microbial dysbiosis associated with primary oral candidiasis and the effects of antifungal therapy, further validation in larger cohorts is warranted.