Changes in the vaginal microbiome during pregnancy and the postpartum period in South African women: a longitudinal study
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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 Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Human immunodeficiency virus (HIV) at Visit B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Visit B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 135
- Group 1 sample size Number of subjects in the case (exposed) group
- 107
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
- Zero-Inflated Negative Binomial Regression
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplement S6
Description: Differential abundance testing of microbial species in women with and without Human immunodeficiency virus, HIV (zero-inflated negative binomial model)
Abundance in Group 1: decreased abundance in Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Visit B
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus jensenii |
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Human immunodeficiency virus (HIV) at Postpartum (PPt) visit
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Postpartum (PPt) visit.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) whose mean gestational age at the postpartum visit was 17 days after delivery.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplement S6
Description: Differential abundance testing of microbial species in women with and without Human Imunodeficiency virus, HIV (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Postpartum (PPt) visit.
| NCBI | Quality Control | Links |
|---|---|---|
| Fannyhessea vaginae | ||
| Metamycoplasma hominis |
Revision editor(s): Tosin
Signature 2
Source: Supplement S6
Description: Differential abundance testing of microbial species in women with and without Human Imunodeficiency virus, HIV (zero-inflated negative binomial model)
Abundance in Group 1: decreased abundance in Pregnant women ≥ 18 years of age with Human immunodeficiency virus (HIV) at Postpartum (PPt) visit.
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella corporis | ||
| Hallella bergensis |
Revision editor(s): Tosin
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sexually transmitted disease disease (VD), venereal,disease, sexually Transmitted,disease, venereal,diseases, sexually Transmitted,diseases, venereal,infection, sexually Transmitted,infections, sexually Transmitted,sexually transmitted disease,sexually Transmitted disorder,sexually Transmitted infection,sexually Transmitted infections,STD,STDs,STI,STIs,Transmitted infection, sexually,Transmitted infections, sexually,VD,VD, venereal disease,venereal disease,venereal disease (VD),venereal diseases,Sexually transmitted disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Visit A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit A
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose mean gestational age at Visit A (first ANC visit) was 18.6 weeks (SD 6.3), with a range of 6–30 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 162
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 a
Description: Differential abundance testing of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit A
| NCBI | Quality Control | Links |
|---|---|---|
| Hallella colorans | ||
| Hoylesella buccalis | ||
| Metamycoplasma hominis | ||
| Prevotella amnii | ||
| Prevotella bivia | ||
| Sneathia vaginalis | ||
| Veillonellaceae bacterium |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Visit B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 a
Description: Differential abundance testing of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Visit B
| NCBI | Quality Control | Links |
|---|---|---|
| Hoylesella buccalis |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without any sexually transmitted infection (STI) at Postpartum (PPt) visit
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Postpartum (PPt) visit.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 a
Description: Differential abundance testing of vaginal microbial species in women with and without any sexually transmitted infection, STI diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with any sexually transmitted infection (STI) at Postpartum (PPt) visit.
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp. |
Revision editor(s): Tosin
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chlamydia trachomatis infectious disease chlamydia,Chlamydia Infections,Chlamydia trachomatis caused disease or disorder,Chlamydia trachomatis disease or disorder,Chlamydia trachomatis infectious disease,chlamydia trachomatis infectious disease,chlamydial disease,Chlamydial Infection,Chlamydial infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at Visit A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit A
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose mean gestational age at Visit A (first ANC visit) was 18.6 weeks (SD 6.3), with a range of 6–30 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 190
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 b
Description: Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit A
| NCBI | Quality Control | Links |
|---|---|---|
| Hallella colorans | ||
| Hoylesella buccalis | ||
| Prevotella amnii | ||
| Sneathia vaginalis | ||
| Veillonellaceae bacterium | ||
| uncultured Megasphaera sp. | ||
| uncultured Lachnospiraceae bacterium |
Revision editor(s): Tosin
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at Visit B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose gestational age range at Visit B (third trimester visit) was 24–36 weeks.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 b
Description: Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at Visit B
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Megasphaera sp. | ||
| Hoylesella buccalis |
Revision editor(s): Tosin
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Chlamydia trachomatis (CT) infection at postpartum (PPt) visit.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at postpartum (PPt) visit
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 b
Description: Differential abundance testing of vaginal microbial species in women with and without Chlamydia trachomatis (CT) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with Chlamydia trachomatis (CT) infection at postpartum (PPt) visit
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp. |
Revision editor(s): Tosin
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gonorrhea Neisseria gonorrhoeae infection,chronic gonococcal infectious disease of lower genitourinary tract,chronic gonococcal infectious disease of upper genitourinary tract,Crosti-gianotti syndrome,Gianotti Crosti syndrome,acrodermatitis, infantile lichenoid,acrodermatitis, papular infantile,infections, Neisseria gonorrhoeae,papular acrodermatitis of childhood,Gonorrhea,gonorrhea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Neisseria gonorrhoea (NG) infection at postpartum (PPt) visit.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Neisseria gonorrhoea (NG) infection at postpartum (PPt) visit
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Neisseria gonorrhoea (NG) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 228
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 c
Description: Differential abundance testing of vaginal microbial species in women with and without Neisseria gonorrhoea (NG) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: decreased abundance in Pregnant women ≥ 18 years of age with Neisseria gonorrhoea (NG) infection at postpartum (PPt) visit
| NCBI | Quality Control | Links |
|---|---|---|
| Hallella bergensis |
Revision editor(s): Tosin
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Trichomonas vaginitis Leukorrhoea vaginalis - trichomonal,Trichomonal leukorrhoea,Trichomonal vaginitis &/or vulvovaginitis,Trichomonal vaginitis (disorder),Trichomonal vulvovaginitis,Trichomonal vulvovaginitis (disorder),Trichomonas vaginalis caused disease of genitourinary system,Trichomonas vaginalis disease of genitourinary system,Trichomonas vaginalis trichomoniasis,Trichomonas Vaginitis,Trichomonas vaginitis,Trichomonas vaginitis urogenital infection,urogenital infection by Trichomonas vaginalis,urogenital infection caused by Trichomonas vaginalis,urogenital Trichomonas,urogenital trichomoniasis,vaginal trichomoniasis (disorder),trichomonas vaginitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Trichomonas vaginalis (TV) infection at Visit A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at Visit A
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection diagnosis whose mean gestational age at Visit A (first ANC visit) was 18.6 weeks (SD 6.3), with a range of 6–30 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 204
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 d
Description: Differential abundance testing of vaginal microbial species in women with and without Trichomonas vaginalis (TV) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: increased abundance in Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at Visit A
| NCBI | Quality Control | Links |
|---|---|---|
| Metamycoplasma hominis |
Revision editor(s): Tosin
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pregnant women ≥ 18 years of age without Trichomonas vaginalis (TV) infection at postpartum (PPt) visit.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at postpartum (PPt) visit
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection diagnosis whose mean gestational age at the postpartum visit was 17 days after delivery.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplement S10 d
Description: Differential abundance testing of vaginal microbial species in women with and without Trichomonas vaginalis (TV) infection diagnosis (zero-inflated negative binomial model)
Abundance in Group 1: decreased abundance in Pregnant women ≥ 18 years of age with Trichomonas vaginalis (TV) infection at postpartum (PPt) visit
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens |
Revision editor(s): Tosin
