Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
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
- Supragingival dental plaque , Saliva Supragingival plaque,Supragingival dental plaque,supragingival 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
- Microbiome measurement Microbiome measurement,microbiome measurement
- 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
- Supragingival 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
- Supragingival plaque samples of children < 72 months of age 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
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- raw counts
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
Source: Table 2
Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group
Abundance in Group 1: increased abundance in Supragingival plaque from severe early childhood caries (S-ECC)
| NCBI | Quality Control | Links |
|---|---|---|
| Candida dubliniensis | ||
| Candida albicans | ||
| Thelephoraceae | ||
| Ramicandelaber taiwanensis | ||
| Fusarium sp. | ||
| Stereum rugosum | ||
| Wallemia tropicalis |
Revision editor(s): Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-6
Source: Table 2
Description: Differential abundance analysis of fungal taxa in supragingival plaque compared to oral swab samples within the S-ECC (severe early childhood caries) group
Abundance in Group 1: decreased abundance in Supragingival plaque from severe early childhood caries (S-ECC)
| NCBI | Quality Control | Links |
|---|---|---|
| Agaricomycetes | ||
| Malassezia restricta | ||
| Trichosporon asahii | ||
| Malassezia globosa |
Revision editor(s): Scholastica
