Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study
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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.
Authors
Wu AH, Tseng C, Vigen C, Yu Y, Cozen W, Garcia AA, Spicer D
Journal
Breast cancer research and treatment
Year
2020
Keywords:
Age at menarche, HER2 status, Microbiome, Tumor characteristics
OBJECTIVE: To investigate the association between gut microbiome with breast tumor characteristics (receptor status, stage and grade) and known breast cancer risk factors. METHODS: In a pilot cross-sectional study of 37 incident breast cancer patients, fecal samples collected prior to chemotherapy were analyzed by 16S ribosomal RNA (rRNA) gene-based sequencing protocol. Alpha diversity and specific taxa by tumor characteristics and breast cancer risk factors were tested by Wilcoxon rank sum test, and by differential abundance analysis, using a zero-inflated negative binomial regression model with adjustment for total counts, age and race/ethnicity. RESULTS: There were no significant alpha diversity or phyla differences by estrogen/progesterone receptor status, tumor grade, stage, parity and body mass index. However, women with human epidermal growth factor receptor 2 positive (HER2+) (n = 12) compared to HER2- (n = 25) breast cancer showed 12-23% lower alpha diversity [number of species (OTU) p = 0.033, Shannon index p = 0.034], lower abundance of Firmicutes (p = 0.005) and higher abundance of Bacteroidetes (p = 0.089). Early menarche (ages ≤ 11) (n = 11) compared with later menarche (ages ≥ 12) (n = 26) was associated with lower OTU (p = 0.036), Chao1 index (p = 0.020) and lower abundance of Firmicutes (p = 0.048). High total body fat (TBF) (> 46%) (n = 12) compared to lower (≤ 46%) TBF was also associated with lower Chao 1 index (p = 0.011). There were other significant taxa abundance differences by HER2 status, menarche age, as well as other tumor and breast cancer risk factors. CONCLUSIONS AND RELEVANCE: Further studies are needed to identify characteristics of the human microbiome and the interrelationships between breast cancer hormone receptor status and established breast cancer risk factors.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/06/21
Curator: Itslanapark
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Itslanapark, Peace Sandy
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
- HER2 Positive Breast Carcinoma ERBB2 Overexpressing subtype of breast carcinoma,HER2 Overexpressing breast carcinoma,HER2 Overexpressing subtype of breast carcinoma,HER2 Positive breast cancer,HER2 positive breast carcinoma,Her2-receptor positive breast cancer,HER2 Positive Breast Carcinoma,hER2 Positive Breast Carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Her2 negative tumor
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Her2 positive tumor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive)
- 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
- 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 found using zero-inflated negative binomial model of taxa abundance by HER2 status
Abundance in Group 1: increased abundance in Her2 positive tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus |
Revision editor(s): Itslanapark
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 3
Description: Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by ER, PR, and HER2 status
Abundance in Group 1: decreased abundance in Her2 positive tumor
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrio | ||
| Ruminococcus | ||
| Christensenellaceae |
Revision editor(s): Itslanapark, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/05
Curator: Itslanapark
Revision editor(s): Itslanapark, LGeistlinger, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age at menarche Age at menarche,age at menarche
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- early age at menarche (≤11)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- later age at menarche (≥12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- breast cancer patients with age at menarche being over 12 years old
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 5
Description: Mean estimate ratios gound using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.
Abundance in Group 1: increased abundance in later age at menarche (≥12)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia |
Revision editor(s): Itslanapark, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 5
Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.
Abundance in Group 1: decreased abundance in later age at menarche (≥12)
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter | ||
| Ruminococcus |
Revision editor(s): Itslanapark
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/05
Curator: Itslanapark
Revision editor(s): Itslanapark, LGeistlinger, WikiWorks
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
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
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): LGeistlinger, Itslanapark, WikiWorks
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
- Grade Low (I/II)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Grade High (III)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- breast cancer patients with grade high level tumors (Grade III)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
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 4
Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.
Abundance in Group 1: increased abundance in Grade High (III)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella |
Revision editor(s): Itslanapark
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 4
Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.
Abundance in Group 1: decreased abundance in Grade High (III)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Anaerostipes |
Revision editor(s): Itslanapark
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer stage Breast cancer stage,breast cancer stage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Stage Low (I/II)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Stage High (III)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients with high stage progression of breast cancer (Stage III).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 4
Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.
Abundance in Group 1: increased abundance in Stage High (III)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Veillonella | ||
| Haemophilus |
Revision editor(s): Itslanapark
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Table 4
Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.
Abundance in Group 1: decreased abundance in Stage High (III)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Catenibacterium |
Revision editor(s): Itslanapark
Experiment 7
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Age 50+
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Age ≤50
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients whose age is ≤50 years old.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- 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 5
Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.
Abundance in Group 1: increased abundance in Age ≤50
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Clostridium | ||
| Enterobacteriaceae | ||
| Lactococcus |
Revision editor(s): Itslanapark
Experiment 8
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parous Parous,parous
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Parous
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nulliparous
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients who are nulliparous (have had no live births.)
- 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
- 8
Lab analysis
Statistical Analysis
- 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 5
Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.
Abundance in Group 1: decreased abundance in Nulliparous
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacterium |
Revision editor(s): Itslanapark
Experiment 9
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body mass index BMI,Quetelet's Index,Body mass index,body mass index
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BMI<25
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BMI≥25
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients with a high body mass index (BMI≥25)
- 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
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
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 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 BMI≥25
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Itslanapark
Experiment 10
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/07
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
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
Experiment 11
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/07/08
Curator: Itslanapark
Revision editor(s): Itslanapark, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Physical activity Activities, Locomotor,Activities, Motor,Activities, Physical,Activity, Locomotor,Activity, Motor,Activity, Physical,Locomotor Activities,Locomotor Activity,Motor Activities,Motor Activity,Physical Activities,Physical activity,physical activity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Yes Physical Activity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- No Physical Activity
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients who do not have regular physical activity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- 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
Statistical Analysis
- 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
- decreased
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