Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- South Africa
- 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
- Contraception contraceptive management,Contraception,contraception
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NET-En (norethisterone enanthate ) arm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COC (combined oral contraceptives) arm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (adolescents) who were randomized to combined oral contraceptives.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure, Confounders controlled for: "condom use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.condom use
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs Net EN (norethisterone enanthate) arm].
Abundance in Group 1: increased abundance in COC (combined oral contraceptives) arm
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus gasseri | ||
| Lactobacillus iners | ||
| Lactobacillus jensenii | ||
| Lactobacillus johnsonii | ||
| Lactobacillus taiwanensis | ||
| Veillonella montpellierensis |
Revision editor(s): Tosin
Signature 2
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover COC (combined oral contraceptives) vs Net EN (norethisterone enanthate ) arm].
Abundance in Group 1: decreased abundance in COC (combined oral contraceptives) arm
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CCVR (combined contraceptive vaginal ring) arm
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs CCVR (combined contraceptive vaginal ring) arm].
Abundance in Group 1: increased abundance in COC (combined oral contraceptives) arm
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus gasseri | ||
| Lactobacillus johnsonii | ||
| Prevotella melaninogenica | ||
| Lactobacillus taiwanensis |
Revision editor(s): Tosin
Signature 2
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs CCVR (combined contraceptive vaginal ring) arm].
Abundance in Group 1: decreased abundance in COC (combined oral contraceptives) arm
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Prevotella amnii |
Revision editor(s): Tosin
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Net-En (norethisterone enanthate) arm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (adolescents) who were randomized to injectable norethisterone enanthate.
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [Net-En (norethisterone enanthate) vs CCVR (combined contraceptive vaginal ring) arm].
Abundance in Group 1: increased abundance in Net-En (norethisterone enanthate) arm
Revision editor(s): Tosin
Signature 2
Source: Table 3A
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [Net-En (norethisterone enanthate) vs CCVR (combined contraceptive vaginal ring) arm].
Abundance in Group 1: decreased abundance in Net-En (norethisterone enanthate) arm
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella | ||
| Gemelliphila asaccharolytica | ||
| Lactobacillus jensenii | ||
| Metamycoplasma hominis | ||
| Prevotella disiens |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline [COC (combined oral contraceptives)] arm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crossover [COC (combined oral contraceptives)] arm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (adolescents) who were randomized to combined oral contraceptives at crossover.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 2
Source: Table 3B
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at Baseline [COC (combined oral contraceptives) vs Crossover [COC (combined oral contraceptives)].
Abundance in Group 1: increased abundance in Crossover [COC (combined oral contraceptives)] arm
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
Signature 3
Source: Table 3B
Description: Deseq2 analysis of taxa differentially abundant between randomized study arms at Baseline [COC (combined oral contraceptives) vs Crossover [COC (combined oral contraceptives)].
Abundance in Group 1: decreased abundance in Crossover [COC (combined oral contraceptives)] arm
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium moniliforme | ||
| Clostridium perfringens |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline [Net-En (norethisterone enanthate)] arm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crossover [Net-En (norethisterone enanthate)] arm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (adolescents) who were randomized to norethisterone enanthate at crossover.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 3B
Description: Deseq2 analysis of taxa differentially abundant between randomized study arms at Baseline [Net-En (norethisterone enanthate) vs Crossover [Net-En (norethisterone enanthate)].
Abundance in Group 1: increased abundance in Crossover [Net-En (norethisterone enanthate)] arm
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Metamycoplasma hominis | ||
| Prevotella disiens |
Revision editor(s): Tosin
