Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- India
- 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
- Spontaneous preterm birth Spontaneous preterm birth,spontaneous preterm birth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Term birth (TB)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Preterm birth (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 140
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Seven days
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Needs review
Source: Figure 7
Description: Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).
Abundance in Group 1: increased abundance in Preterm birth (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners | ||
| Pseudomonas sp. | ||
| Fannyhessea vaginae | ||
| Prevotella corporis | ||
| Sneathia sanguinegens |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 7
Description: Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).
Abundance in Group 1: decreased abundance in Preterm birth (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus crispatus | ||
| Lactobacillus johnsonii |
Revision editor(s): Rahila
