Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women/Experiment 7
From BugSigDB
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 , Saliva 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,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer , Breast ductal carcinoma in situ 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,breast ductal carcinoma in situ,carcinoma in situ of mammary duct,DCIS,ductal breast carcinoma in situ,ductal carcinoma in situ,ductal carcinoma in situ (DCIS),ductal carcinoma in situ of breast,ductal carcinoma in situ of the breast,intraductal breast carcinoma,intraductal carcinoma,intraductal carcinoma of breast,intraductal carcinoma of the breast,mammary duct carcinoma in situ,mammary duct in situ carcinoma,non-infiltrating ductal adenocarcinoma of breast,non-infiltrating ductal adenocarcinoma of the breast,non-infiltrating ductal breast adenocarcinoma,non-infiltrating ductal breast carcinoma,non-infiltrating ductal carcinoma of breast,non-infiltrating ductal carcinoma of the breast,non-infiltrating intraductal adenocarcinoma,non-infiltrating intraductal adenocarcinoma of breast,non-infiltrating intraductal adenocarcinoma of the breast,non-infiltrating intraductal breast adenocarcinoma,non-infiltrating intraductal carcinoma,non-invasive ductal adenocarcinoma of breast,non-invasive ductal adenocarcinoma of the breast,non-invasive ductal breast adenocarcinoma,non-invasive ductal breast carcinoma,non-invasive ductal carcinoma of breast,non-invasive ductal carcinoma of the breast,non-invasive intraductal adenocarcinoma of breast,non-invasive intraductal adenocarcinoma of the breast,non-invasive intraductal breast adenocarcinoma,stage 0 mammary duct carcinoma,Breast ductal carcinoma in situ
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Oral
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gut
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diversity comparisons of gut vs. oral microbiota.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Supplementary Figure S5C
Description: LEfSe analysis comparing gut and oral microbiota at the genus (C) levels. The top 10 differentially abundant taxa, based on LDA score, are shown.
Abundance in Group 1: increased abundance in Gut
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Ruminococcus | ||
| Lachnospira | ||
| Akkermansia |
Revision editor(s): Rahila
Signature 2
Source: Supplementary Figure S5C
Description: LEfSe analysis comparing gut and oral microbiota at the genus (C) levels. The top 10 differentially abundant taxa, based on LDA score, are shown.
Abundance in Group 1: decreased abundance in Gut
| NCBI | Quality Control | Links |
|---|---|---|
| Selenomonas | ||
| Granulicatella | ||
| Veillonella | ||
| Neisseria | ||
| Haemophilus | ||
| Streptococcus |
Revision editor(s): Rahila
