Breast cancer but not the menopausal status is associated with small changes of the gut microbiota
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Zeber-Lubecka N, Kulecka M, Jagiełło-Gruszfeld A, Dąbrowska M, Kluska A, Piątkowska M, Bagińska K, Głowienka M, Surynt P, Tenderenda M, Mikula M, Ostrowski J
Journal
Frontiers in oncology
Year
2024
Keywords:
breast cancer, gut dysbiosis, menopausal status, microbiome, shotgun
BACKGROUND: Possible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls. RESULTS: Firstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively. CONCLUSION: While our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.
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
- 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 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
- pre-menopausal controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-menopausal BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newly diagnosed pre- or perimenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Antibiotic use within 2 months before fecal sampling
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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Linear 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
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table 3
Description: Taxa differentiating premenopausal BC patients from premenopausal controls assessed using the LInear model for Differential Abundance (LINDA) method for compositional data, and p-values were corrected using the Benjamini–Hochberg.
Abundance in Group 1: increased abundance in pre-menopausal BC patients
Revision editor(s): Keamy
Signature 2
Source: Table 3
Description: Taxa differentiating premenopausal BC patients from premenopausal controls assessed using the LInear model for Differential Abundance (LINDA) method for compositional data, and p-values were corrected using the Benjamini–Hochberg.
Abundance in Group 1: decreased abundance in pre-menopausal BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacter |
Revision editor(s): Keamy
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- post-menopausal controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-menopausal BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table 4
Description: Taxa differentiating postmenopausal BC patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data, and p-values were corrected using the Benjamini–Hochberg.
Abundance in Group 1: increased abundance in post-menopausal BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella intestinalis | ||
| Agathobaculum butyriciproducens | ||
| Agathobaculum | ||
| Harryflintia | ||
| Enterorhabdus | ||
| Rothia | ||
| Allisonella | ||
| Micrococcaceae |
Revision editor(s): Keamy
Signature 2
Source: Table 4
Description: Taxa differentiating postmenopausal BC patients from postmenopausal controls assessed using the LInear model for Differential Abundance (LINDA) method for compositional data, and p-values were corrected using the Benjamini–Hochberg.
Abundance in Group 1: decreased abundance in post-menopausal BC patients
Revision editor(s): Keamy
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-menopausal controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-menopausal controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
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
- increased
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-menopausal BC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-menopausal BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal Breast Cancer Patients.
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
Experiment 5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-menopausal stage 0-2 BC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pre-menopausal stage 3 BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre or Perimenopausal Stage 3 Breast Cancer Patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- 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
Signature 1
Source: Table 5
Description: Taxa differentiating premenopausal patients with stage 3 BC from other premenopausal BC patients assessed using the LInear model for Differential Abundance (LINDA) method for compositional data, and p-values were corrected using the Benjamini–Hochberg.
Abundance in Group 1: decreased abundance in pre-menopausal stage 3 BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia equolifaciens | ||
| Adlercreutzia equolifaciens subsp. celatus | ||
| Firmicutes bacterium CAG:110 |
Revision editor(s): Keamy
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- post-menopausal stage 0-2 BC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-menopausal stage 3 BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal Stage 3 Breast Cancer Patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
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
- decreased
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Other Pre- or perimenopausal BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pre- or perimenopausal TNBC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pre- or perimenopausal Triple-negative Breast Cancer Patients differentiated from patients with other hormone receptor statuses.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
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
- decreased
Experiment 8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Postmenopausal BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postmenopausal TNBC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal Triple-negative Breast Cancer Patients differentiated from patients with other hormone receptor statuses.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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
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