Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
Curated date: 2024/04/21
Curator: Rahila
Revision editor(s): WikiWorks, Scholastica, Rahila, Taofeecoh
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
- Saliva , Supragingival dental plaque Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Supragingival plaque,Supragingival dental plaque,supragingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dental caries caries,CARIES DENT,Caries, Dental,DECAY DENT,Decay, Dental,DENT CARIES,DENT DECAY,DENT WHITE SPOT,DENT WHITE SPOTS,dental caries,dental caries extending into pulp,dental caries of smooth surface,dental caries pit and fissure,Dental Decay,Dental White Spot,Dental White Spots,Spot, White,Spots, White,White Spot,WHITE SPOT DENT,White Spot, Dental,White Spots,WHITE SPOTS DENT,White Spots, Dental,Dental caries
- 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
- Supragingival plaque from caries-free
- 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 who are caries-free, confirmed by a dental examination
- 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).
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
Source: FIG. 3C
Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group
Abundance in Group 1: increased abundance in Supragingival plaque from caries-free
Revision editor(s): Rahila, Scholastica, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-5
Source: FIG. 3C
Description: Differential abundance analysis of species that were overabundant in supragingival plaque compared to oral swab samples within the caries-free group
Abundance in Group 1: decreased abundance in Supragingival plaque from caries-free
Revision editor(s): Rahila, Scholastica, WikiWorks
