Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

Abstract

The human oral cavity harbors one of the most diverse microbial communities with different oral microenvironments allowing the colonization of unique microbial species. This study aimed to determine which of two commonly used sampling sites (dental plaque vs. oral swab) would provide a better prediction model for caries-free vs. severe early childhood caries (S-ECC) using next generation sequencing and machine learning (ML). In this cross-sectional study, a total of 80 children (40 S-ECC and 40 caries-free) < 72 months of age were recruited. Supragingival plaque and oral swab samples were used for the amplicon sequencing of the V4-16S rRNA and ITS1 rRNA genes. The results showed significant differences in alpha and beta diversity between dental plaque and oral swab bacterial and fungal microbiomes. Differential abundance analyses showed that, among others, the cariogenic species Streptococcus mutans was enriched in the dental plaque, compared to oral swabs, of children with S-ECC. The fungal species Candida dubliniensis and C. tropicalis were more abundant in the oral swab samples of children with S-ECC compared to caries-free controls. They were also among the top 20 most important features for the classification of S-ECC vs. caries-free in oral swabs and for the classification of dental plaque vs. oral swab in the S-ECC group. ML approaches revealed the possibility of classifying samples according to both caries status and sampling sites. The tested site of sample collection did not change the predictability of the disease. However, the species considered to be important for the classification of disease in each sampling site were slightly different. Being able to determine the origin of the samples could be very useful during the design of oral microbiome studies. This study provides important insights into the differences between the dental plaque and oral swab bacteriome and mycobiome of children with S-ECC and those caries-free.

The Crosstalk Between Saliva Bacteria and Fungi in Early Childhood Caries

“…The limitations above remind us of a larger-scale cohort and the employment of whole metagenome sequencing and metabolomics analysis in future studies. Although saliva samples are easy to collect, the distinctive taxonomic profiles between saliva and dental plaque have been observed in previous research (Cui et al, 2021;de Jesus et al, 2021), suggesting a further investigation of plaque microorganisms in predicting ECC, for the closer contact of plaque with the dental surface may result in a higher sensitivity in predicting ECC compared with that of saliva samples. Besides, attention need to be paid to the cross-kingdom interactions in ECC progression, and the mechanisms of Neocosmospora in inhibiting cariogenic taxa are worthy of future investigation.…”

“…In the current study, we investigated the salivary bacterial and fungal profiles in children with good oral health, ECC, and SECC. Most studies involving ECC were largely focused on oral bacteria or pathogenic C. albicans (Xiao et al, 2018;Alkhars et al, 2021;Baker et al, 2021;de Jesus et al, 2021).…”

“…The clinical validity and convenience of saliva test have been well suggested ( Zhang et al., 2016 ; Kaczor-Urbanowicz et al., 2019 ; Fernandes et al., 2020 ), while the dental explorer which is used for plaque collecting may cause fear and anxiety in children ( Leal et al., 2013 ), leaving a more preferable test method of saliva to kids. So far, the only few published studies involving whole oral mycobiome and ECC were either focusing solely on a fungal community without referring to oral bacteria ( Fechney et al., 2019 ; Cui et al., 2021 ) or using dental plaque or oral swab samples ( de Jesus et al., 2020 ; de Jesus et al., 2021 ). Hence, in the current study, we intended to 1) capture the saliva microbial (bacterial and fungal) community variation in different oral health status, 2) identify potential microbial biomarkers of healthy and ECC status, and 3) uncover the interaction between the oral microbiome and mycobiome in caries development.…”

Determinants and Interactions of Oral Bacterial and Fungal Microbiota in Healthy Chinese Adults

“…An ASV belonging to the genus Blumeria represents another potential fungal keystone taxon in the oral microbiome of healthy adults. An unidentified species of Blumeria has also been detected in high abundance in dental plaque of caries-free children ( 61 ). However, additional information of Blumeria species in the oral cavity are scarce to date.…”

Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis

“…Amplicon sequence variants (ASVs) were aligned with Mafft and Fasttree2 was used to make a phylogeny tree [27]. Taxonomic assignment of ASVs was performed with the classify-sklearn naïve Bayes taxonomy classifier against the eHOMD database (HOMD, version 15.1, Cambridge, MA, USA) [26,[28][29][30]. Only taxa with non-zero counts in at least 5% of the samples were retained.…”