Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis/Experiment 3
From BugSigDB
Needs review
Subjects
- Location of subjects
- Singapore
- 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
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva,Gingivitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women with gingivitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: increased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: decreased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
