Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2024/01/10

Curator: ChiomaBlessing

Revision editor(s): 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
Prediagnostic (PD)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Tumor (T)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples donated after breast cancer diagnosis (tumor)
Group 0 sample size Number of subjects in the control (unexposed) group
15
Group 1 sample size Number of subjects in the case (exposed) group
46

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
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged