Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues
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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
- Morocco
- 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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- 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
- Adjacent normal tissue of BC patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor tissue of BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of tumor tissues without any contamination of normal tissues.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- 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)
- 3 months
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
Signature 1
Source: Figure 1 (C)
Description: Significant biomarkers between the tumor and adjacent tissues performed by linear discriminant analysis effect size (LEfSe) scores.
Abundance in Group 1: increased abundance in Tumor tissue of BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Finegoldia | ||
| Peptostreptococcales_TissierellalesPeptostreptococcales_Tissierellales |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 1 (C)
Description: Significant biomarkers between the tumor and adjacent tissues performed by linear discriminant analysis effect size (LEfSe) scores.
Abundance in Group 1: decreased abundance in Tumor tissue of BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadaceae | ||
| Pseudomonas |
Revision editor(s): Ecsharp
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure 3 (A-E)
Description: Individual differences in proportional abundances of the most significantly altered microbial communities between adjacent and breast tumor tissues at different levels. A p < 0.05 is considered statistically significant based on t-test measurements.
Abundance in Group 1: decreased abundance in Tumor tissue of BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bdellovibrionota | ||
| Oligoflexia | ||
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Genus 0319-6G20Genus 0319-6G20 |
Revision editor(s): Ecsharp
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Luminal B breast carcinoma Luminal B,Luminal B breast cancer,Luminal B breast carcinoma,Luminal B estrogen receptor positive subtype of breast carcinoma,Luminal B subtype of breast carcinoma,luminal B breast carcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BC patients with Luminal B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of Luminal B tumor tissues without any contamination of normal tissues.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4. (A)
Description: Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.
Abundance in Group 1: increased abundance in BC patients with Luminal B
| NCBI | Quality Control | Links |
|---|---|---|
| Alloiococcus |
Revision editor(s): Ecsharp
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Luminal A breast carcinoma Luminal A,Luminal A breast cancer,Luminal A breast carcinoma,Luminal A estrogen receptor positive subtype of breast carcinoma,Luminal A subtype of breast carcinoma,luminal A breast carcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BC patients with Luminal A
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of Luminal A tumor tissues without any contamination of normal tissues.
- 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
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4. (A)
Description: Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.
Abundance in Group 1: increased abundance in BC patients with Luminal A
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4. (A)
Description: Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.
Abundance in Group 1: decreased abundance in BC patients with Luminal A
| NCBI | Quality Control | Links |
|---|---|---|
| Lawsonella |
Revision editor(s): Ecsharp
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triple-negative breast cancer triple-negative breast cancer,triple-negative breast carcinoma,triple-receptor negative breast cancer,Triple-negative breast cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BC patients with TNBC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer (BC) patients were pathologically diagnosed with primary BC and underwent surgery for a total or partial mastectomy. Tumor tissue samples were obtained from the cores of triple-negative breast cancer (TNBC) tumor tissues without any contamination of normal tissues.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4. (A)
Description: Individual differences in proportional abundances of significantly altered microbial genus between adjacent and breast tumor tissues in the hormonal patients’ groups. A p < 0.05 is considered statistically significant based on t-test measurements.
Abundance in Group 1: decreased abundance in BC patients with TNBC
| NCBI | Quality Control | Links |
|---|---|---|
| Sporosarcina |
Revision editor(s): Ecsharp
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triple-negative breast cancer , HER2 Positive Breast Carcinoma triple-negative breast cancer,triple-negative breast carcinoma,triple-receptor negative breast cancer,Triple-negative breast cancer,ERBB2 Overexpressing subtype of breast carcinoma,HER2 Overexpressing breast carcinoma,HER2 Overexpressing subtype of breast carcinoma,HER2 Positive breast cancer,HER2 positive breast carcinoma,Her2-receptor positive breast cancer,HER2 Positive Breast Carcinoma,hER2 Positive Breast Carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BC patients with HER2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
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: Figure 4 (B)
Description: LDA score computed on the microbial relative abundance between breast tumor subtypes. The TNBC group is illustrated as Group 1, and the HER2 group as Group 2.
Abundance in Group 1: decreased abundance in BC patients with TNBC
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Caldimonas | ||
| Thermales | ||
| Thermus | ||
| Deinococcota | ||
| Thermaceae | ||
| Deinococci |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4 (B)
Description: LDA score computed on the microbial relative abundance between breast tumor subtypes. The TNBC group is illustrated as Group 1, and the HER2 group as Group 2.
Abundance in Group 1: increased abundance in BC patients with TNBC
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingomonadaceae | ||
| Sphingomonadales |
Revision editor(s): Ecsharp
