The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study

Abstract

Background: The oral fungal microbiome (mycobiome) is not well characterized, particularly in relation to oral diseases such as periodontal disease. We aimed to describe and compare the oral mycobiome of subjects with and without periodontal disease.

Results: We characterized the oral mycobiome in 30 adult subjects (15 with periodontal disease, 15 with good oral health) by sequencing the taxonomically informative pan-fungal internal transcribed spacer (ITS) gene in DNA extracted from oral wash samples. We observed at least 81 genera and 154 fungal species across all samples. Candida and Aspergillus were the most frequently observed genera (isolated from 100% of participants), followed by Penicillium (97%), Schizophyllum (93%), Rhodotorula (90%), and Gibberella (83%). Candida and Aspergillus were also the most highly abundant genera in the samples (median relative abundance = 21% and 44%, respectively). Aspergillus niger was the most highly abundant species in the samples (median relative abundance = 44%). We did not observe significant differences in overall oral mycobiome diversity or composition between participants with periodontal disease and participants with good oral health, nor did we observe significant differences in phylum through species level taxon relative abundance or carriage between the two groups. Genus Candida, previously associated with periodontal disease in culture-based studies, had higher median relative abundance in participants with periodontal disease (33.2%) compared to participants with oral health (2.2%), though the difference was not significant (p = 0.52). Additionally, within the periodontal disease group, median relative abundance of Candida increased with increasing number of permanent teeth lost (1-2 teeth lost: 3.2%; 3-4 teeth lost: 16.6%; ≥5 teeth lost: 73.9%; p = 0.11), though sample size was small for this analysis.

Conclusions: In this first study comprehensively characterizing the oral mycobiome of adults with periodontal disease or good oral health, we observed trends of higher Candida abundance in participants with periodontal disease, and participants with greater tooth loss. Small sample size may have limited the power to detect significant associations. Larger studies including subgingival samples may further establish the core oral mycobiome in health, and relate it to periodontal disease.

Keywords: Fungus; ITS; Mycobiome; Oral; Periodontal disease; Periodontitis.

Conflict of interest statement

Ethics approval and consent to participate

The study described in this manuscript was approved by the institutional review board of the NYU School of Medicine, and all participants provided written informed consent (IRB study number: i12-00855).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1

Pie chart showing the frequency (%) of sequence reads belonging to each fungal phylum from 30 oral wash samples

Fig. 2

a Frequency and b relative abundance of fungal genera in oral wash samples. In (a), all unidentified genera were grouped into one bar, and all other genera are shown individually. In (b), only the 23 most abundant genera are shown

Fig. 3

a Frequency and b relative abundance of fungal species in oral wash samples. In (a), all unidentified species were grouped into one bar, and all other species present in at least two people are shown individually. In (b), only the 23 most abundant species are shown

Fig. 4

Rarefaction curves of (a) richness and (b) evenness. These indices were calculated for 100 iterations of rarefied OTU tables, and the average over the iterations was taken for each participant. Means are shown for the periodontal disease and oral health groups

Fig. 5

Principal coordinate analysis of the Jensen-Shannon Divergence (JSD). The first two coordinates are plotted. Shapes outlined in black represent centroids for periodontal disease and oral health groups

Fig. 6

a Relative abundance of genus Candida and Candida species in participants with periodontal disease or oral health and b relative abundance of genus Candida by number of permanent teeth lost