Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study/Experiment 3
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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/05
Curator: Itslanapark
Revision editor(s): WikiWorks, LGeistlinger, 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
- Estrogen receptor status Estrogen receptor status,estrogen receptor status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ER+
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ER-
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- breast cancer patients with negative Estrogen Receptor status
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Antibiotic use one week or more during the month prior to fecal sample collection.
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, ethnic group, race, Confounders controlled for: "total counts" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.total counts
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 3
Description: Mean ratio estimates obtained by zero-inflated negative binomial model of taxa abundances by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status.
Abundance in Group 1: decreased abundance in ER-
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Veillonella |
Revision editor(s): Itslanapark
