Site-Specific Profiling of the Dental Mycobiome Reveals Strong Taxonomic Shifts during Progression of Early-Childhood Caries

Abstract

Dental caries is one of the most common diseases worldwide. Bacteria and fungi are both commensals in the oral cavity; however, most research regarding caries has focused on bacterial impacts. The oral fungal mycobiome associated with caries is not well characterized, and its role in disease is unclear. ITS1 amplicon sequencing was used to generate taxonomic profiles from site-specific supragingival plaque samples (n = 82) obtained from 33 children with different caries status. Children were either caries free (CF), caries active with enamel lesions (CAE), or caries active with dentin lesions (CA). Plaque samples were collected from caries-free surfaces (PF) and from enamel (PE) and dentin (PD) lesions. Taxonomic profiles representing the different categorizations (CF-PF, CAE-PF, CAE-PE, CA-PF, CA-PE, and CA-PD) were used to characterize the mycobiome and its change through disease progression. A total of 139 fungal species were identified. Candida albicans was the most abundant species, followed by Candida dubliniensis. We found that severely progressed plaque communities (CA-PD) were significantly different from healthy plaque communities (CF-PF). A total of 32 taxa were differentially abundant across the plaque categories. C. albicans, C. dubliniensis, Nigrospora oryzae, and an unclassified Microdochium sp. were correlated with caries, whereas 12 other taxa were correlated with health. C. dubliniensis increased steadily as caries progressed, suggesting that C. dubliniensis may play an important role in caries pathogenicity. In contrast, four health-associated fungal taxa have the potential to antagonize the cariogen Streptococcus mutans via xylitol production, suggesting a possible fungal mechanism that could contribute to maintenance of dental health. IMPORTANCE Early-childhood caries is one of the most prevalent diseases in children worldwide and, while preventable, remains a global public health concern. Untreated cavities are painful and expensive and can lead to tooth loss and a lower quality of life. Caries are driven by acid production via microbial fermentation of dietary carbohydrates, resulting in enamel erosion. While caries is a well-studied disease, most research has focused on bacterial impacts, even though fungi are commensal organisms living within the plaque biofilm. There is very little known about how fungi impact caries pathogenicity. The elucidation of fungal taxa involved in caries disease progression is necessary for a more holistic view of the human oral microbiome. Data from this study will improve our understanding of how the fungal community changes as disease progresses and provide insight into the complex etiology of dental caries, which is necessary for the development of treatment plans and preventative measures.

Critically Appraising the Significance of the Oral Mycobiome

“…The role of the oral mycobiome in caries has been the focus of recent research. Several mycobiome studies have explored fungal community diversity in relation to caries in children (Fechney et al 2019; Baraniya et al 2020; de Jesus et al 2020; O’Connell et al 2020). Studies that compared the oral mycobiome between caries-free and caries-affected children with mixed dentition reported differences in abundance of certain fungi according to caries status.…”

“…This study also reported differences in the mycobiome and its relationship to caries according to sex, with caries-free females showing an enrichment of Malassezia restricta . In a site-specific analysis of the mycobiome associated with ECC, caries-free children were compared to those with lesions in enamel or dentin, also discriminating between healthy surfaces, sites with enamel caries, and dentin lesions (O’Connell et al 2020). This study showed a trend for decreased mycobiome diversity as caries severity increased and found C. albicans and C. dubliniensis were positively correlated with caries.…”

“… Twenty-one original research articles evaluating the oral mycobiome were included (a, Abusleme et al 2018; b, Annavajhala et al 2020; c, Baraniya et al 2020; d, Cui et al 2015; e, de Jesus et al 2020; f, Dupuy et al 2014; g, El Jurdi et al 2019; h, Fechney et al 2019; i, Ghannoum et al 2010; j, Hong et al 2020; k, Ieda et al 2014; l, Imabayashi et al 2016; m, Li et al 2019; n, Mukherjee et al 2014; o, Mukherjee et al 2018; p, O’Connell et al 2020; q, Peters et al 2017; r, Robinson et al 2020; s, Shelburne et al 2015; t, Ward et al 2018; u, Watkins et al 2016). Fungi were considered in the tally if they appeared in the main figures and tables of the manuscript. ITS-1, internal transcribed spacer 1; MS, mucosal swab; OR, oral rinse; SA, saliva; SUB, subgingival plaque; SUP, supragingival plaque. …”

Streptococcus mutans Membrane Vesicles Harboring Glucosyltransferases Augment Candida albicans Biofilm Development

“…A number of studies have reported that C. albicans can often be detected with S. mutans in ECC dental plaque samples, and the detection rate of C. albicans is significantly higher in children with ECC than in caries-free children ( Yang et al, 2012 ; Xiao et al, 2018a , b ). High-throughput amplicon sequencing was used to characterize the oral microbiome associated with ECC, and the results indicated that C. albicans was the most abundant fungus and correlated with caries ( O’Connell et al, 2020 ). Therefore, C. albicans , as a part of dental plaque, can enhance the virulence of plaque biofilms and is considered to be an important factor in ECC ( Hajishengallis et al, 2017 ; Koo et al, 2018 ).…”

Effect of Polyols and Selected Dental Materials on the Ability to Create a Cariogenic Biofilm–On Children Caries-Associated Streptococcus Mutans Isolates

“…Fluoride prophylaxis in the form of toothpastes, mouth rinses, professional fluoride treatment, and dental cavity filling with fluoride-releasing materials is a widely used strategy to prevent caries. However, due to the large role of dietary factors in its pathogenesis, it is important to replace sucrose-rich foods with foods lacking simple sugars or with natural sucrose substitutes such as xylitol, sorbitol, or erythritol, additionally characterized by cariostatic properties [16,21].…”