Breast cancer but not the menopausal status is associated with small changes of the gut microbiota/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-6-13
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- post-menopausal controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-menopausal BC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Newly diagnosed postmenopausal breast cancer patients at the Maria Sklodowska-Curie National Research Institute of Oncology.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Linear Regression
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-13
Source: Table 4
Description: Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data
Abundance in Group 1: increased abundance in post-menopausal BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobaculum | ||
| Collinsella intestinalis | ||
| Harryflintia | ||
| Micrococcaceae |
Revision editor(s): Keamy, Scholastica, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-13
Source: Table 4
Description: Taxa differentiating postmenopausal breast cancer (BC) patients from postmenopausal controls assessed using the Linear model for Differential Abundance (LINDA) method for compositional data
Abundance in Group 1: decreased abundance in post-menopausal BC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides thetaiotaomicron | ||
| Barnesiellaceae | ||
| Blautia obeum | ||
| Coprobacter | ||
| Coprobacter fastidiosus | ||
| Dorea | ||
| Parabacteroides | ||
| Parabacteroides distasonis | ||
| Phascolarctobacterium faecium |
Revision editor(s): Keamy, Scholastica, WikiWorks
