Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study/Experiment 10
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria
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
- 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
- Body fat percentage Body fat percentage,body fat percentage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TBF≤46%
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TBF>46%
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients with a total body fat percentage ≥46%.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 6
Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.
Abundance in Group 1: increased abundance in TBF>46%
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae |
Revision editor(s): Itslanapark
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 6
Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.
Abundance in Group 1: decreased abundance in TBF>46%
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae |
Revision editor(s): Itslanapark
