Comprehensive profiles and diagnostic value of menopausal-specific gut microbiota in premenopausal breast cancer
-
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
- Taiwan
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast carcinoma breast cancer,breast cancer, NOS,breast carcinoma,cancer of breast,cancer of the breast,cancer, breast,carcinoma of breast,carcinoma of the breast,mammary carcinoma,Breast carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal female controls (Pre-C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- premenopausal breast cancer patients (Pre-BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Premenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: FIG 2 (B)
Description: Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C)
Abundance in Group 1: increased abundance in premenopausal breast cancer patients (Pre-BC)
Revision editor(s): Rahila, Scholastica
Signature 2
Source: FIG 2 (B)
Description: Significantly differential gut microbiota in premenopausal breast cancer (Pre-BC) patients compared to premenopausal female controls (Pre-C)
Abundance in Group 1: decreased abundance in premenopausal breast cancer patients (Pre-BC)
Revision editor(s): Rahila, Scholastica
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Postmenopausal female controls (Post-C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal breast cancer patients (Post-BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: FIG 2 (C)
Description: Significantly differential gut microbiota in postmenopausal breast cancer (Post-BC) patients compared to postmenopausal female controls (Post-C)
Abundance in Group 1: increased abundance in Postmenopausal breast cancer patients (Post-BC)
Revision editor(s): Rahila, Scholastica
Signature 2
Source: FIG 2 (C)
Description: Significantly differential gut microbiota in postmenopausal breast cancer (Post-BC) patients compared to postmenopausal female controls (Post-C)
Abundance in Group 1: decreased abundance in Postmenopausal breast cancer patients (Post-BC)
Revision editor(s): Rahila, Scholastica
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Menopause Change of Life, Female,Menopause,menopause
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal female controls (Pre-C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal female controls (Post-C)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal female controls (Post-C) participants
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: FIG 2 (A)
Description: Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C)
Abundance in Group 1: increased abundance in Postmenopausal female controls (Post-C)
| NCBI | Quality Control | Links |
|---|---|---|
| Synergistales | ||
| Synergistia | ||
| Amedibacillus dolichus |
Revision editor(s): Scholastica
Signature 2
Source: FIG 2 (A)
Description: Significantly differential gut microbiota in premenopausal female controls (Pre-C) compared to postmenopausal female controls (Post-C)
Abundance in Group 1: decreased abundance in Postmenopausal female controls (Post-C)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Actinomycetota | ||
| Faecalibacterium | ||
| Bifidobacterium | ||
| Faecalibacterium prausnitzii | ||
| Bifidobacterium adolescentis | ||
| Bifidobacterium longum |
Revision editor(s): Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal breast cancer patients (Pre-BC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal breast cancer patients (Post-BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal breast cancer patients diagnosed with stage I–II disease by pathological examination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: FIG 3 (C)
Description: Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients
Abundance in Group 1: increased abundance in Postmenopausal breast cancer patients (Post-BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptophyta | ||
| Turicibacteraceae | ||
| Candidatus Tariuqbacterales | ||
| Gammaproteobacteria | ||
| Desulfovibrio | ||
| Turicibacter | ||
| Ruminococcus callidus | ||
| Veillonella dispar |
Revision editor(s): Scholastica
Signature 2
Source: FIG 3 (C)
Description: Significantly differential gut microbiota in premenopausal (Pre-BC) compared to postmenopausal breast cancer (Post-BC) patients
Abundance in Group 1: decreased abundance in Postmenopausal breast cancer patients (Post-BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Actinomycetota | ||
| Bifidobacterium | ||
| Oscillospira | ||
| Bilophila | ||
| Adlercreutzia | ||
| Roseburia faecis | ||
| Bifidobacterium adolescentis | ||
| Bifidobacterium longum |
Revision editor(s): Scholastica
