Increased diversity of a cervical microbiome associates with cervical cancer
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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
- Poland
- 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
- Uterine cervix 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
- Response to radiation Response to radiation,response to radiation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal healthy controls (HPV Negative women)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Premenopausal Pre-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- 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
- V2-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: increased abundance in Premenopausal Pre-treatment group
Revision editor(s): Joan Chuks
Signature 2
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: decreased abundance in Premenopausal Pre-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Aminobacter | ||
| Cutibacterium | ||
| Escherichia/Shigella sp. | ||
| Lactobacillus | ||
| Pseudomonas | ||
| Rheinheimera | ||
| Staphylococcus |
Revision editor(s): Joan Chuks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Postmenopausal healthy controls (HPV Negative women)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal Pre-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
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
- unchanged
Signature 1
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: increased abundance in Postmenopausal Pre-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Arcanobacterium | ||
| Fusobacterium | ||
| Moryella | ||
| Peptococcus | ||
| Peptoniphilus | ||
| Porphyromonas | ||
| Stomatobaculum |
Revision editor(s): Joan Chuks
Signature 2
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: decreased abundance in Postmenopausal Pre-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella | ||
| Gemella | ||
| Lentilitoribacter | ||
| Mesorhizobium |
Revision editor(s): Joan Chuks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal healthy controls (HPV Negative women)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Premenopausal Post-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table S2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.
Abundance in Group 1: increased abundance in Premenopausal Post-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus | ||
| Campylobacter | ||
| Clostridiales bacterium S5-A14a | ||
| Corynebacterium | ||
| Dialister | ||
| Finegoldia | ||
| Peptoniphilus | ||
| Peptostreptococcus | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): Joan Chuks
Signature 2
Source: Supplementary Table S2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.
Abundance in Group 1: decreased abundance in Premenopausal Post-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Aminobacter | ||
| Bifidobacterium | ||
| Brucella | ||
| Granulicatella | ||
| Hoeflea | ||
| Ottowia | ||
| Parabacteroides | ||
| Pluralibacter |
Revision editor(s): Joan Chuks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Postmenopausal healthy controls (HPV Negative women)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal Post-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table S2
Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.
Abundance in Group 1: increased abundance in Postmenopausal Post-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Caulobacter | ||
| Diaphorobacter | ||
| Porphyromonas | ||
| Renibacterium | ||
| Sphingomonas | ||
| Methylobacterium-MethylorubrumMethylobacterium-Methylorubrum |
Revision editor(s): Joan Chuks
Signature 2
Source: Supplementary Table S2
Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.
Abundance in Group 1: decreased abundance in Postmenopausal Post-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella | ||
| Lentilitoribacter | ||
| Mesorhizobium |
Revision editor(s): Joan Chuks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-treatment group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
Signature 1
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: increased abundance in Post-treatment group
Revision editor(s): Joan Chuks
Signature 2
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: decreased abundance in Post-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Bulleidia | ||
| Fusobacterium | ||
| Olsenella | ||
| Peptococcus | ||
| Porphyromonas | ||
| Prevotella | ||
| Solobacterium | ||
| Stomatobaculum |
Revision editor(s): Joan Chuks
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 3-months post treatment group (follow-up samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), 3 months after the last fraction of brachytherapy (ICBT) was given.
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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
Signature 1
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: increased abundance in 3-months post treatment group (follow-up samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Finegoldia |
Revision editor(s): Joan Chuks
Signature 2
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT), compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: decreased abundance in 3-months post treatment group (follow-up samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium |
Revision editor(s): Joan Chuks
