Microbiota composition in bilateral healthy breast tissue and breast tumors/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
