Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester/Experiment 1
Subjects
- Location of subjects
- Egypt
- 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 orifice Introitus,Introitus of vagina,Opening of vagina,Orifice of vagina,Ostium vaginae,Vagina opening,Vaginal introitus,Vaginal orifice,Vagina orifice,vagina orifice
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Streptococcal infection infection, streptococcal,infections, streptococcal,streptococcal infection,Streptococcal Infections,Streptococcus caused disease or disorder,Streptococcus disease or disorder,Streptococcus infectious disease,Streptococcal infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GBS culture-negative pregnant women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GBS culture-positive pregnant women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women whose culture status shows group B Streptococcus (GBS) to be Positive
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within the previous six months
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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: (Figs. 3 and 4 panels A, B, C, and D).
Description: Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing biomarker phylum (A), family (B), genus (C), and species (D) with significant differential abundance in GBS culture-negative and GBS culture-positive pregnant Egyptian women using SILVA database. FDR adjusted p values and LDA score > 2 was considered statistically significant. Not_Assigned refers to taxa that were challenging for biological interpretation
Abundance in Group 1: decreased abundance in GBS culture-positive pregnant women
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Lactobacillus iners | ||
| Lactobacillus iners AB-1 | ||
| Limosilactobacillus coleohominis |
Revision editor(s): Ayibatari
Signature 2
Source: (Figs. 3 and 4 panels A, B, C, and D).
Description: Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing biomarker phylum (A), family (B), genus (C), and species (D) with significant differential abundance in GBS culture-negative and GBS culture-positive pregnant Egyptian women using SILVA database. FDR adjusted p values and LDA score > 2 was considered statistically significant. Not_Assigned refers to taxa that were challenging for biological interpretation
Abundance in Group 1: increased abundance in GBS culture-positive pregnant women
Revision editor(s): Ayibatari
