Microbiota composition in bilateral healthy breast tissue and breast tumors
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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
- United States of America
- 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
- Bilateral Normal Breast Tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tumor Breast Tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer tumor tissue samples from white, non-Hispanic women, obtained through the University of Florida (UF) Clinical and Translational Sciences Institute (CTSI) Biorepository
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4
Description: Significantly different taxa identified by differential abundance between normal and tumor tissue. All OTUs shown were found to be statistically significant in terms of differential abundance using Wald’s test with Benjamini–Hochberg adjustment in the DESeq2 package (DESeq function).
Abundance in Group 1: increased abundance in Tumor Breast Tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides | ||
| Butyricimonas | ||
| Faecalibacterium | ||
| Holdemania | ||
| Oscillospira | ||
| Parabacteroides | ||
| Rothia | ||
| Ruminococcus | ||
| Staphylococcus | ||
| Sutterella | ||
| Varibaculum |
Revision editor(s): Ecsharp
Signature 2
Source: Figure 4
Description: Significantly different taxa identified by differential abundance between normal and tumor tissue. All OTUs shown were found to be statistically significant in terms of differential abundance using Wald’s test with Benjamini–Hochberg adjustment in the DESeq2 package (DESeq function).
Abundance in Group 1: decreased abundance in Tumor Breast Tissue
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).
- log transformation
- Statistical test
- MaAsLin2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Online Resource 3
Description: A total of 131 OTUs were identified as significantly associated with tissue group (normal or tumor) through a generalized linear mixed effects model with individual subject as the random effect and disease status as the fixed effect. The most specific level of taxonomic classification is reported for each OTU. A positive coefficient indicates the OTU is more abundant in normal tissue and a negative coefficient indicates the OTU is more abundant in tumor tissue.
Abundance in Group 1: increased abundance in Tumor Breast Tissue
Revision editor(s): Ecsharp
Signature 2
Source: Online Resource 3
Description: A total of 131 OTUs were identified as significantly associated with tissue group (normal or tumor) through a generalized linear mixed effects model with individual subject as the random effect and disease status as the fixed effect. The most specific level of taxonomic classification is reported for each OTU. A positive coefficient indicates the OTU is more abundant in normal tissue and a negative coefficient indicates the OTU is more abundant in tumor tissue.
Abundance in Group 1: decreased abundance in Tumor Breast Tissue
Revision editor(s): Ecsharp
Experiment 3
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Online Resources 1a-c
Description: Relative abundance of phyla, families, and genera in normal and tumor tissue. P-values were generated using a non-parametric Mann-Whitney U test and were adjusted using the Benjamini-Hochberg method.
Abundance in Group 1: increased abundance in Tumor Breast Tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Butyricimonas | ||
| Odoribacteraceae | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Verrucomicrobiaceae | ||
| Verrucomicrobiota |
Revision editor(s): Ecsharp
Signature 2
Source: Online Resources 1a-c
Description: Relative abundance of phyla, families, and genera in normal and tumor tissue. P-values were generated using a non-parametric Mann-Whitney U test and were adjusted using the Benjamini-Hochberg method.
Abundance in Group 1: decreased abundance in Tumor Breast Tissue
Revision editor(s): Ecsharp
