Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- 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 (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Breast cancer (BC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)
- 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
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Antibiotic use within four weeks of 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)
- 0.05
- 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
- body mass index, race, sex
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
Source: Figure 3
Description: Bacteria significantly increased in patients with breast cancer compared to healthy controls. (a–f) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 6 features were significantly higher in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ .15). Significance: * < 0.05 and ** < 0.01.
Abundance in Group 1: increased abundance in Breast cancer (BC)
NCBI | Quality Control | Links |
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Actinomyces | ||
Blautia | ||
Eggerthella | ||
Faecalitalea | ||
Intestinibacter bartlettii | ||
Oscillospiraceae |
Revision editor(s): ChiomaBlessing, Peace Sandy
Signature 2
Source: Figure 4
Description: Bacteria significantly decreased in patients with breast cancer compared to healthy controls. (a–h) Based on the Wilcoxon test and the Benjamini–Hochberg procedure, 8 features weresignificantly lower in abundance in the breast cancer cohort compared to the healthy controls (p ≤ 0.05, q ≤ 0.15). Significance: * < 0.05, ** < 0.01, and *** < 0.001.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
Revision editor(s): ChiomaBlessing, Peace Sandy