Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues/Experiment 6
From BugSigDB
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
- 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 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
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- 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
- 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 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
