Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria/Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca mulatta
- 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
- Clinical laboratory measurement clinical laboratory techniques,Clinical laboratory measurement,clinical laboratory measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- health-control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- gut bacterial dysbiosis in breast cancer could lead to refned prevention and treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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)
- 0.0001
- 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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- sex, age
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
Source: Figure 3
Description: Bacteria signifcantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were signifcantly higher in abundance in the breast cancer cohort compared to the healthy controls (p≤0.05, q≤.15). Signifcance: *<0.05 and **<0.01.
Abundance in Group 1: increased abundance in Breast cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Acidobacteriota | ||
| Blastocatellia |
Revision editor(s): Som252
Signature 2
Source: Figure 3
Description: Bacteria significantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were significantly higher in abundance in the breast cancer cohort compared to the healthy controls (p≤0.05, q≤.15). Significance: *<0.05 and **<0.01.
Abundance in Group 1: decreased abundance in Breast cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Acidobacteriota | ||
| Blastocatellia |
Revision editor(s): Som252
