Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2021/09/16
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
- Pregnancy Gestation,PREGN,Pregnancies,Pregnancy,pregnancy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women sampled between 21 to 24 wk of gestation without 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
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Source: Appendix Figure 1, 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: increased abundance in pregnant women without gingivitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Fusobacteriia | ||
| Fusobacterium | ||
| Spirochaetota | ||
| Treponema | ||
| Candidatus Saccharibacteria |
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Source: Appendix Figure 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: decreased abundance in pregnant women without gingivitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Gemella | ||
| Haemophilus | ||
| Streptococcus | ||
| Terrahaemophilus |
