Vaginal Microbiome in Pregnant Women with and without Short Cervix/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-12
Subjects
- Location of subjects
- Italy
- 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
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervix erosion cervix erosion,Erosion of cervix,erosion of cervix,Erosion of cervix (disorder),Uterine Cervical Erosion,Cervix erosion
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Short Cervix Length
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women of predominantly Caucasian ethnicity with singleton gestation and a cervical length ≤ 25 mm in their second or early third trimester (23–32 weeks’ gestation)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- At the time of recruitment
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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)
- 0.05
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-12
Source: Figure 2a
Description: Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels
Abundance in Group 1: increased abundance in Short Cervix Length
Revision editor(s): Ayibatari, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-12
Source: Figure 2a
Description: Linear discriminant analysis effect size (LEfSe) showing the significant taxonomic features in short cervix length versus control groups at different taxonomic levels
Abundance in Group 1: decreased abundance in Short Cervix Length
| NCBI | Quality Control | Links |
|---|---|---|
| Paracoccaceae | ||
| Rhodobacterales | ||
| Actinomycetales | ||
| Actinomycetaceae | ||
| Clostridia | ||
| Paracoccus | ||
| Porphyromonas | ||
| Porphyromonadaceae | ||
| Micrococcales | ||
| Mobiluncus |
Revision editor(s): Scholastica
