Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ, Chelikani P
Journal
Frontiers in microbiology
Year
2021
Keywords:
artificial intelligence, bacteria, case-control, dental plaque, fungi, machine learning, microbiota, oral swab
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.
Experiment 1
Subjects
- Location of subjects
- Canada
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Dental plaque , Saliva Bacterial plaque,Plaque,Dental plaque,dental plaque,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Mouth disease disease of mouth,disease of the mouth,disease or disorder of mouth,disorder of mouth,mouth disease,mouth disease or disorder,mouth disorder,oral cavity disease,oral cavity disorder,oral disease,oral disorder,Mouth disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral swab from severe early childhood caries (S-ECC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dental plaque from severe early childhood caries (S-ECC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The differences between the dental plaque and oral swab bacteriome and mycobiome of children with severe early childhood caries (S-ECC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Use of antibiotics
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: FIG 3 (B)
Description: Relative fold change in the abundance of bacterial species in (B) samples from children with S-ECC, according to sample type(Plaque)
Abundance in Group 1: increased abundance in Dental plaque from severe early childhood caries (S-ECC)
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (B)
Description: Relative fold change in the abundance of bacterial species in (B) samples from children with S-ECC, according to sample type (Swab).
Abundance in Group 1: decreased abundance in Dental plaque from severe early childhood caries (S-ECC)
Revision editor(s): Rahila
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral swab from Caries-free
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dental plaque from Caries-free
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The differences between the dental plaque and oral swab bacteriome and mycobiome of children that are in the Caries-free groups
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: FIG 3 (C)
Description: Relative fold change in the abundance of bacterial species in (C) samples from caries-free children, according to sample type (Plaque).
Abundance in Group 1: increased abundance in Dental plaque from Caries-free
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (C)
Description: Relative fold change in the abundance of bacterial species in (C) samples from caries-free children, according to sample type (Swab).
Abundance in Group 1: decreased abundance in Dental plaque from Caries-free
Revision editor(s): Rahila
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