Urinary and oral microbiota in Polish women: a pilot case-control study of breast cancer/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Poland
- 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 (BC) cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BC cases, regardless of subtype, with biological samples collected between 2004 and 2006 from 5 Regional Cancer Registries located in Poland
- 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
- 24
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, region of residence
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, menopause, smoking status, alcohol drinking
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4
Description: Log 2 Fold changes of urine bacterial abundance between cases and healthy controls at different taxonomic levels
Abundance in Group 1: increased abundance in Breast cancer (BC) cases
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadales | ||
| Pseudomonadaceae | ||
| unclassified Gammaproteobacteria | ||
| Pseudomonas | ||
| uncultured Pseudomonas sp. | ||
| uncultured Gammaproteobacteria bacterium |
Revision editor(s): Ecsharp
