Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
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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
- France
- 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
- Tumor stage tumour stage,Tumor stage,tumor stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-CT Stage I
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre-CT Stage II/III
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients before chemotherapy with TNM Stage II/III
- 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
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- relative abundances
- Statistical test
- PLS-DA (Partial least square discriminant analysis)
- 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
Signature 1
Source: Fig. 1B
Description: Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue)
Abundance in Group 1: increased abundance in Pre-CT Stage II/III
Revision editor(s): Scholastica
Signature 2
Source: Fig. 1B
Description: Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Pre-CT TNM stage I (orange) compared to Pre-CT TNM stage II-III (blue)
Abundance in Group 1: decreased abundance in Pre-CT Stage II/III
Revision editor(s): Scholastica
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post-CT Stage I
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-CT Stage II/III
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after chemotherapy with TNM Stage II/III
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 1E
Description: Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue)
Abundance in Group 1: increased abundance in Post-CT Stage II/III
Revision editor(s): Scholastica
Signature 2
Source: Fig. 1E
Description: Variable importance plot (VIP) scores obtained within partial least square discriminant analysis describing the most discriminant species in Post-CT TNM stage I (orange) compared to Post-CT TNM stage II-III (blue)
Abundance in Group 1: decreased abundance in Post-CT Stage II/III
Revision editor(s): Scholastica
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tumor size size of tumor,Tumor size,tumor size
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-Chemo tumor size <pT1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre-Chemo tumor size >pT1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients before chemotherapy with pathological tumor size greater than pT1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S2B
Description: Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1
Abundance in Group 1: increased abundance in Pre-Chemo tumor size >pT1
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S2B
Description: Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy with tumor size <pT1 versus tumor size >pT1
Abundance in Group 1: decreased abundance in Pre-Chemo tumor size >pT1
Revision editor(s): Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post-Chemo tumor size <pT1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Chemo tumor size >pT1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after chemotherapy with pathological tumor size greater than pT1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S2D
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1
Abundance in Group 1: increased abundance in Post-Chemo tumor size >pT1
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S2D
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy with tumor size <pT1 versus tumor size >pT1
Abundance in Group 1: decreased abundance in Post-Chemo tumor size >pT1
Revision editor(s): Scholastica
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tumor grading Tumor grading,tumor grading
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SBR Gr1/2 Post-Chemo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SBR Gr3 Post-Chemo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after chemotherapy with Scarff Bloom & Richardson (SBR) grade Gr3
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S3C
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3
Abundance in Group 1: increased abundance in SBR Gr3 Post-Chemo
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S3C
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to tumor histological grade SBR; Gr1/2 compared to Gr3
Abundance in Group 1: decreased abundance in SBR Gr3 Post-Chemo
Revision editor(s): Scholastica
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tumor stage tumour stage,Tumor stage,tumor stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pN- pre-Chemo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pN+ pre-Chemo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients before chemotherapy with positive axillary lymph node involvement
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S4B
Description: Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)
Abundance in Group 1: increased abundance in pN+ pre-Chemo
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S4B
Description: Metagenomics analyses of stool samples from early breast cancer patients before chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)
Abundance in Group 1: decreased abundance in pN+ pre-Chemo
Revision editor(s): Scholastica
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pN- post-Chemo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pN+ post-Chemo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after chemotherapy with positive axillary lymph node involvement
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S4D
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)
Abundance in Group 1: increased abundance in pN+ post-Chemo
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S4D
Description: Metagenomics analyses of stool samples from early breast cancer patients after chemotherapy according to axillary lymph node involvement: positive lymph node (pN+, blue dots) versus negative lymph node (pN-, orange dots)
Abundance in Group 1: decreased abundance in pN+ post-Chemo
Revision editor(s): Scholastica
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer breast cancer,breast tumor,cancer of breast,malignant breast neoplasm,malignant breast tumor,malignant neoplasm of breast,malignant neoplasm of the breast,malignant tumor of breast,malignant tumor of the breast,mammary cancer,mammary neoplasm,mammary tumor,primary breast cancer,Breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy volunteers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients enrolled in the CANTO study
- Group 0 sample size Number of subjects in the control (unexposed) group
- 336
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Fig. 2A
Description: Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method
Abundance in Group 1: increased abundance in Breast cancer patients
Revision editor(s): Scholastica
Signature 2
Source: Fig. 2A
Description: Metagenomics analyses of stool samples from breast cancer patients compared with healthy volunteers (HV) using LEfSe method
Abundance in Group 1: decreased abundance in Breast cancer patients
Revision editor(s): Scholastica
Experiment 9
Subjects
- Location of subjects
- France
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tumor stage tumour stage,Tumor stage,tumor stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoadjuvant_pN-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Neoadjuvant_pN+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after neoadjuvant chemotherapy treatment with pathological lymph node involvement
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 2
Lab analysis
Statistical Analysis
- Statistical test
- PLS-DA (Partial least square discriminant analysis)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Fig. 2D
Description: Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)
Abundance in Group 1: increased abundance in Neoadjuvant_pN+
Revision editor(s): Scholastica
Signature 2
Source: Fig. 2D
Description: Metagenomics analyses of stool samples from BC patients comparing species abundance according to the pathological lymph node involvement (no pathological lymph node involvement, pN-, orange; versus pathological lymph node involvement, pN+, blue) in stools collected after neoadjuvant CT (n = 10)
Abundance in Group 1: decreased abundance in Neoadjuvant_pN+
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia obeum | ||
| Dorea formicigenerans | ||
| Fusicatenibacter saccharivorans | ||
| Roseburia inulinivorans | ||
| Phocaeicola vulgatus |
Revision editor(s): Scholastica
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoadjuvant stage post-Chemo (Stage 0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Neoadjuvant stage post-Chemo (Stage I/II)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after neoadjuvant chemotherapy treatment who are pathological non-complete responders (stage I–II)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S3D
Description: Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II)
Abundance in Group 1: increased abundance in Neoadjuvant stage post-Chemo (Stage I/II)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterocloster citroniae |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S3D
Description: Metagenomics analyses of stool samples from early BC patients treated in a neoadjuvant setting comparing pathological complete responders (stage I) to non-complete responders (stage I–II)
Abundance in Group 1: decreased abundance in Neoadjuvant stage post-Chemo (Stage I/II)
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella sanguinis | ||
| Streptococcus mitis | ||
| Eubacterium ventriosum |
Revision editor(s): Scholastica
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to combination chemotherapy Response to combination chemotherapy,response to combination chemotherapy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-Chemotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Chemotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients after Chemotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Source: Fig. 3C
Description: Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy
Abundance in Group 1: increased abundance in Post-Chemotherapy
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemanella biformis | ||
| [Ruminococcus] torques | ||
| Dorea formicigenerans | ||
| Firmicutes bacterium CAG:110 | ||
| Methanobrevibacter smithii |
Revision editor(s): Scholastica
Signature 2
Source: Fig. 3C
Description: Differentially significant abundant taxa in breast cancer patients pre-Chemotherapy compared to post-Chemotherapy
Abundance in Group 1: decreased abundance in Post-Chemotherapy
Revision editor(s): Scholastica
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Adverse effect adverse reaction,Adverse effect,adverse effect
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No - increased BMI (Pre-Chemo)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yes - increased BMI (Pre-Chemo)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients before Chemotherapy with increased Body Mass Index (BMI)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Fig. S6B
Description: Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI
Abundance in Group 1: increased abundance in Yes - increased BMI (Pre-Chemo)
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S6B
Description: Differentially significant abundant taxa in breast cancer patients before Chemotherapy with increased BMI compared to those without increased BMI
Abundance in Group 1: decreased abundance in Yes - increased BMI (Pre-Chemo)