Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9
Curated date: 2023/10/29
Curator: OdigiriGreat
Revision editor(s): OdigiriGreat, LGeistlinger, ChiomaBlessing
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
- Healthy (H)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prediagnostic (PD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples donated prior to breast cancer diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 49
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9
Source: Figure 3b
Description: Differentially abundant taxa in Prediagnostic group versus Healthy group
Abundance in Group 1: increased abundance in Prediagnostic (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Caldimonas | ||
| Fusobacterium | ||
| Pantoea | ||
| Romboutsia | ||
| Sphingomonas | ||
| Staphylococcus | ||
| Streptococcus sp. |
Revision editor(s): OdigiriGreat, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9
Source: Figure 3b
Description: Differentially abundant taxa in Prediagnostic group versus Healthy group
Abundance in Group 1: decreased abundance in Prediagnostic (PD)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium |
Revision editor(s): OdigiriGreat, ChiomaBlessing
