Breast tissue, oral and urinary microbiomes in breast cancer/Experiment 2
From BugSigDB
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
- Urine Urine,urine
- 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 controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- breast cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients eligible were over 18 years of age, female, had tumors greater than or equal to 2 cm in size, were undergoing mastectomy. Patients receiving neo-adjuvant therapy prior to surgery or with active clinical breast infection were excluded from the study.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- 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
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- menopause
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Cancer vs. Non-Cancer Samples Independent of Menopausal Status
Abundance in Group 1: increased abundance in breast cancer patients
Revision editor(s): Ecsharp
