Mining the oral mycobiome: Methods, components, and meaning.

Area of Science:

• Microbiology
• Genomics
• Oral Biology

Background:

• Research on oral fungi has historically focused on Candida species.
• Recent advancements in DNA sequencing have uncovered a broader spectrum of fungal taxa in the oral cavity.

Purpose of the Study:

• To review DNA-based studies of the oral mycobiome.
• To contrast molecular findings with traditional cultivation-based surveys.
• To discuss challenges in DNA-based oral mycobiome research.

Main Methods:

• Review of internal transcribed spacer (ITS)-based molecular studies.
• Comparison with cultivation-based surveys of oral fungi.
• Analysis of technical and bioinformatic challenges in ITS sequencing.

Main Results:

• Molecular methods have identified a vast number of fungal taxa, significantly expanding the known oral mycobiome.
• Most cultivated oral fungal genera were also detected molecularly.
• Some taxa, notably Malassezia, show high prevalence in molecular studies but remain uncultivated.

Conclusions:

• DNA-based surveys provide a powerful initial characterization of the oral mycobiome.
• Significant technical and bioinformatic challenges persist in ITS-based studies.
• Further research is essential to validate the role of DNA-detected fungi as true oral residents and their impact on oral homeostasis.