Mining the oral mycobiome: Methods, components, and meaning

Abstract

Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis.

The oral microbiome in oral lichen planus during a 1‐year randomized clinical trial

“…In 2014, it was discovered that Malassezia is a predominant oral fungus genus in the mouth and that the relative abundance varied between 13% and 98% in saliva samples from healthy individuals (Dupuy, David, Li, Heider, Peterson et al, ). New sequencing methods allow for more in‐depth analysis of bacterial and fungal components of the oral microbiome, but for the time being, knowledge of the oral mycobiome is less complete than that of the bacteriome due to lower fungal biomass (Diaz, Hong, Dupuy, & Strausbaugh, ; Moon & Lee, ).…”

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

“…Fungi account for a relatively small percentage of the human microbiota, with 10 5 to 10 6 fungal cells per gram of fecal matter (compared to 10 11 bacterial cells per gram) [11] and only 0.1% of the 9.9 million reference genes in a current human gut microbial metagenomic reference catalog are reported to be of eukaryotic origin [12,13]. Additionally, the identification of composition and diversity of the fungal community is influenced by the nucleic acid isolation method [14], the choice of sequencing primer pairs [15], as well as different sequencing technologies [16,17] and bioinformatics pipelines [18,19]. Finally, the incomplete databases for taxonomic assignment and annotation of fungal genomes present a serious difficulty in studying the human mycobiome [15].…”

“…Additionally, the identification of composition and diversity of the fungal community is influenced by the nucleic acid isolation method [14], the choice of sequencing primer pairs [15], as well as different sequencing technologies [16,17] and bioinformatics pipelines [18,19]. Finally, the incomplete databases for taxonomic assignment and annotation of fungal genomes present a serious difficulty in studying the human mycobiome [15]. The usual molecular target for identifying fungi are the internal transcribed spacer (ITS) regions of ribosomal RNA genes.…”

Role of EphA2 in host defense against oro-pharyngeal candidiasis

“…The oral cavity is continuously exposed to a heterogeneous microbiota consisting of bacteria, virus and yeasts interacting with epithelial cells. A vast number of fungal species (up to 100) have been detected in the oral cavity by molecular methods over the last years [1][2][3]. It is clear that Candida, and in particular Candida albicans, is a true inhabitant of the oral cavity in many of us [4], but C. albicans can become pathogenic in vulnerable patients.…”