Diversity of vaginal microbiome and metabolome during genital infections
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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
- Italy
- 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
- 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
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chlamydia trachomatis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ‘Chlamydia’ (CT) (detection of C. trachomatis DNA by Versant CT/GC DNA 1.0 Assay)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- n/a
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
- Kruskall-Wallis
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Table 2
Description: Differential microbial abundance between controls and chlamydia subjects
Abundance in Group 1: increased abundance in Chlamydia trachomatis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Vulvovaginal candidiasis Candidal vulvovaginitis,candidal vulvovaginitis,Candidal vulvovaginitis (disorder),Candidal vulvovaginitis NOS (disorder),Candidal: [vulvovaginitis NOS] or [cervix],candidal: [vulvovaginitis NOS] or [cervix],candidal: cervix,Candidiasis of vulva and vagina,candidiasis of vulva and vagina,Candidiasis, Vulvovaginal,Monilial vulvovaginitis,monilial vulvovaginitis,vaginal candidiasis,Vulvovaginal Candidiasis,vulvovaginal candidiasis,Vulvovaginal candidiasis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vulvovaginal candidiasis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- vulvovaginal candidiasis (VVC)
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Table 2
Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects
Abundance in Group 1: decreased abundance in Vulvovaginal candidiasis
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Lactobacillaceae | ||
Lactobacillus |
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Signature 2
Source: Table 2
Description: Differential microbial abundance between controls and vulvovaginal candidiasis subjects
Abundance in Group 1: increased abundance in Vulvovaginal candidiasis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bacterial vaginosis BACT VAGINITIDES,BACT VAGINITIS,BACT VAGINOSES,BACT VAGINOSIS,Bacterial Vaginitides,Bacterial Vaginitis,Bacterial Vaginoses,bacterial vaginosis,BV,Nonspecific Vaginitis,VAGINITIDES BACT,Vaginitides, Bacterial,VAGINITIS BACT,Vaginitis, Bacterial,Vaginitis, Nonspecific,VAGINOSES BACT,Vaginoses, Bacterial,VAGINOSIS BACT,Vaginosis, Bacterial,Bacterial vaginosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- bacterial vaginosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- bacterial vaginosis (BV)
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Table 2
Description: Differential microbial abundance between controls and bacterial vaginosis subjects
Abundance in Group 1: decreased abundance in bacterial vaginosis
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Lactobacillaceae | ||
Lactobacillus |
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1
Signature 2
Source: Table 2
Description: Differential microbial abundance between controls and bacterial vaginosis subjects
Abundance in Group 1: increased abundance in bacterial vaginosis
Revision editor(s): Danyab56, Aiyshaaaa, Claregrieve1