Alterations in the vaginal microbiota of patients with preterm premature rupture of membranes/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-11
Subjects
- Location of subjects
- China
- 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
- Anterior fornix of vagina , Lateral fornix of vagina , Uterine cervix Anterior fornix,Anterior part of fornix of vagina,Pars anterior fornicis vaginae,Anterior fornix of vagina,anterior fornix of vagina,Lateral part of fornix of vagina,Pars lateralis fornicis vaginae,Lateral fornix of vagina,lateral fornix of vagina,Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Preterm premature rupture of the membranes PPROM,preterm premature rupture of the membranes,Preterm premature rupture of the membranes
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control(term delivery)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Preterm premature rupture of membranes (PPROM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PPROM is characterized by vaginal microbial dysbiosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, gestational age
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- 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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-11
Source: Fig.2C
Description: Differences in bacterial abundance in patients with PPROM versus controls.
Abundance in Group 1: increased abundance in Preterm premature rupture of membranes (PPROM)
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella vaginalis | ||
| Hoylesella timonensis | ||
| Lactobacillus iners | ||
| Ochrobactrum sp. | ||
| Prevotella bivia | ||
| Ureaplasma parvum |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-11
Source: Fig.2C
Description: Differences in bacterial abundance in patients with PPROM versus controls.
Abundance in Group 1: decreased abundance in Preterm premature rupture of membranes (PPROM)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus crispatus | ||
| Lactobacillus gasseri |
