Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Curated date: 2023/10/06
Curator: Joan Chuks
Revision editor(s): Joan Chuks, ChiomaBlessing, Victoria
Subjects
- Location of subjects
- Ireland
- 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
- Posterior fornix of vagina , External cervical os Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina,External os,External os of uterus,Ostium of uterus,Ostium uteri,External cervical os,external cervical os
- 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
- Full-term Birth
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Preterm Birth
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women who delivered before 37 weeks’ gestation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Women currently on antibiotic treatment.
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- raw counts
- Statistical test
- Linear Regression
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Source: Figure 2b + Figure 2C
Description: Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB)
Abundance in Group 1: increased abundance in Preterm Birth
Revision editor(s): Joan Chuks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Source: Figure 2b + Figure 2C
Description: Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB)
Abundance in Group 1: decreased abundance in Preterm Birth
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve | ||
| Lactobacillus crispatus | ||
| Lactobacillus gasseri ATCC 33323 = JCM 1131 | ||
| Lactobacillus johnsonii |
Revision editor(s): Joan Chuks, ChiomaBlessing
