Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
McCune E, Sharma A, Johnson B, O'Meara T, Theiner S, Campos M, Heditsian D, Brain S, Gilbert JA, Esserman L, Campbell MJ
Journal
mSystems
Year
2024
Keywords:
DCIS, breast cancer, gut microbiota, oral microbiota
UNLABELLED: This study characterized and compared the fecal and oral microbiota from women with early-stage breast cancer (BC), women with ductal carcinoma in situ (DCIS), and healthy women. Fecal and oral samples were collected from newly diagnosed patients prior to any therapy and characterized using 16S rRNA sequencing. Measures of gut microbial alpha diversity were significantly lower in the BC vs healthy cohort. Beta diversity differed significantly between the BC or DCIS and healthy groups, and several differentially abundant taxa were identified. Clustering (non-negative matrix factorization) of the gut microbiota identified five bacterial guilds dominated by Prevotella, Enterobacteriaceae, Akkermansia, Clostridiales, or Bacteroides. The Bacteroides and Enterobacteriaceae guilds were significantly more abundant in the BC cohort compared to healthy controls, whereas the Clostridiales guild was more abundant in the healthy group. Finally, prediction of functional pathways identified 23 pathways that differed between the BC and healthy gut microbiota including lipopolysaccharide biosynthesis, glycan biosynthesis and metabolism, lipid metabolism, and sphingolipid metabolism. In contrast to the gut microbiomes, there were no significant differences in alpha or beta diversity in the oral microbiomes, and very few differentially abundant taxa were observed. Non-negative matrix factorization analysis of the oral microbiota samples identified seven guilds dominated by Veillonella, Prevotella, Gemellaceae, Haemophilus, Neisseria, Propionibacterium, and Streptococcus; however, none of these guilds were differentially associated with the different cohorts. Our results suggest that alterations in the gut microbiota may provide the basis for interventions targeting the gut microbiome to improve treatment outcomes and long-term prognosis. IMPORTANCE: Emerging evidence suggests that the gut microbiota may play a role in breast cancer. Few studies have evaluated both the gut and oral microbiomes in women with breast cancer (BC), and none have characterized these microbiomes in women with ductal carcinoma in situ (DCIS). We surveyed the gut and oral microbiomes from women with BC or DCIS and healthy women and identified compositional and functional features of the gut microbiota that differed between these cohorts. In contrast, very few differential features were identified in the oral microbiota. Understanding the role of gut bacteria in BC and DCIS may open up new opportunities for the development of novel markers for early detection (or markers of susceptibility) as well as new strategies for prevention and/or treatment.
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 women (Control)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: FIG 2 (A)
Description: Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Actinomycetota | ||
| Tissierellaceae | ||
| Mycoplasmatota | ||
| Finegoldia |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (A)
Description: Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Bacillota | ||
| Clostridia | ||
| Coprococcus | ||
| Lachnospiraceae | ||
| Eubacteriales |
Revision editor(s): Rahila
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast ductal carcinoma in situ 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 1 name Corresponds to the case (exposed) group for case-control studies
- Ductal carcinoma in situ (DCIS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with ductal carcinoma in situ (DCIS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (B)
Description: Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Acidimicrobiia | ||
| Actinomycetales | ||
| Megamonas | ||
| Actinomycetaceae | ||
| Corynebacteriaceae | ||
| Corynebacterium | ||
| Varibaculum | ||
| Dialister |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospiraceae |
Revision editor(s): Rahila
Experiment 3
Differences from previous experiment shown
Subjects
- 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
- Ductal carcinoma in situ (DCIS)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (C)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Megamonas |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (C)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of gut microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Actinomycetaceae |
Revision editor(s): Rahila
Experiment 4
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy women (Control)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (D)
Description: Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (A)
Description: Identification of microbial taxa that differentiate breast cancer (BC) and healthy groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Coprococcus | ||
| Lachnospiraceae | ||
| Bacillota | ||
| Eubacteriales | ||
| Clostridia |
Revision editor(s): Rahila
Experiment 5
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast ductal carcinoma in situ 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 1 name Corresponds to the case (exposed) group for case-control studies
- Ductal carcinoma in situ (DCIS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with ductal carcinoma in situ (DCIS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (E)
Description: Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Epsilonproteobacteria | ||
| Campylobacterales | ||
| Campylobacteraceae | ||
| Campylobacter |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Identification of microbial taxa that differentiate ductal carcinoma in situ (DCIS) and healthy groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Lachnospiraceae |
Revision editor(s): Rahila
Experiment 6
Differences from previous experiment shown
Subjects
- 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
- Ductal carcinoma in situ (DCIS)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 2 (C)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Megamonas |
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Identification of microbial taxa that differentiate BC and DCIS groups of oral microbiota using LEfSe discriminant analysis.
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Epsilonproteobacteria | ||
| Campylobacterales | ||
| Campylobacteraceae | ||
| Campylobacter |
Revision editor(s): Rahila
Experiment 7
Differences from previous experiment shown
Subjects
- 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.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
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
Experiment 8
Differences from previous experiment shown
Subjects
- 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
- Mammographic density measurement Mammographic density measurement,mammographic density measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low breast density
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High breast density
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Comparing high and low breast density.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: FIG 6 (C)
Description: Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).
Abundance in Group 1: increased abundance in High breast density
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Phascolarctobacterium | ||
| Cyanobacteriota | ||
| 4C0d-24C0d-2 | ||
| YS2YS2 |
Revision editor(s): Rahila
Signature 2
Source: FIG 6 (C)
Description: Differentially enriched taxa abundance in fecal samples between high and low breast density was identified using LEfSe analysis (logarithmic LDA score threshold = 3; P < 0.05).
Abundance in Group 1: decreased abundance in High breast density
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae |
Revision editor(s): Rahila
Experiment 9
Differences from previous experiment shown
Subjects
- 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 women (Control)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Signature 1
Source: FIG 3 (A)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and healthy cohort
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Anaerococcus | ||
| Bacteroides | ||
| Coprobacillus | ||
| Corynebacterium | ||
| Eggerthella | ||
| Finegoldia | ||
| Parabacteroides | ||
| Peptoniphilus | ||
| Streptococcus | ||
| WALWAL |
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (A)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and healthy cohort
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes |
Revision editor(s): Rahila
Experiment 10
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast ductal carcinoma in situ 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 1 name Corresponds to the case (exposed) group for case-control studies
- Ductal carcinoma in situ (DCIS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with ductal carcinoma in situ (DCIS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 3 (B)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between DCIS and healthy cohort
Abundance in Group 1: increased abundance in Ductal carcinoma in situ (DCIS)
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (B)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between DCIS and healthy cohort
Abundance in Group 1: decreased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Rahila
Experiment 11
Differences from previous experiment shown
Subjects
- 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
- Ductal carcinoma in situ (DCIS)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: FIG 3 (C)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort
Abundance in Group 1: increased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium |
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (C)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the gut microbiota between BC and DCIS cohort
Abundance in Group 1: decreased abundance in Breast cancer (BC)
| NCBI | Quality Control | Links |
|---|---|---|
| Varibaculum | ||
| 1-681-68 | ||
| Anaerostipes | ||
| Actinomyces | ||
| Peptoniphilus | ||
| Finegoldia | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Odoribacter | ||
| Dialister | ||
| Veillonella | ||
| Coprococcus |
Revision editor(s): Rahila
Experiment 12
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy women (Control)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Experiment 13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast ductal carcinoma in situ 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 1 name Corresponds to the case (exposed) group for case-control studies
- Ductal carcinoma in situ (DCIS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with ductal carcinoma in situ (DCIS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 3 (E)
Description: DESeq2 differential abundance analysis. Volcano plots of log2 fold differences in genera abundance in the oral microbiota between DCIS and healthy cohort
Abundance in Group 1: decreased abundance in Ductal carcinoma in situ (DCIS)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Blautia |
Revision editor(s): Rahila
Experiment 14
Differences from previous experiment shown
Subjects
- 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
- Ductal carcinoma in situ (DCIS)
- 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
- Women with early-stage of breast cancer (BC),
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
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