Breast tissue, oral and urinary microbiomes in breast cancer
From BugSigDB
Jump to:navigation, search
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 Uniform resource identifier for web resources.
Authors
Wang H, Altemus J, Niazi F, Green H, Calhoun BC, Sturgis C, Grobmyer SR, Eng C
Journal
Oncotarget
Year
2017
Keywords:
breast cancer, metagenomics, microbiome, oral, urine
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- breast cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Breast cancer patients eligible were over 18 years of age, female, had tumors greater than or equal to 2 cm in size, were undergoing mastectomy. Patients receiving neo-adjuvant therapy prior to surgery or with active clinical breast infection were excluded from the study.
- 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
- 39
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
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 4: A) Breast Tissue
Description: Taxa Significantly Different in Cancer vs. Non-Cancer Samples by Wilcoxon Rank Sum
Abundance in Group 1: increased abundance in breast cancer patients
Revision editor(s): Ecsharp
Signature 2
Source: Supplementary Table 4: A) Breast Tissue
Description: Taxa Significantly Different in Cancer vs. Non-Cancer Samples by Wilcoxon Rank Sum
Abundance in Group 1: decreased abundance in breast cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacteriaceae | ||
| Corynebacterium | ||
| Atopobium | ||
| Methylobacterium | ||
| Methylobacteriaceae | ||
| Catonella | ||
| Gemellaceae | ||
| Order GemellalesOrder Gemellales |
Revision editor(s): Ecsharp
Experiment 2
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Urine Urine,urine
- 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
- 46
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- menopause
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Cancer vs. Non-Cancer Samples Independent of Menopausal Status
Abundance in Group 1: increased abundance in breast cancer patients
Revision editor(s): Ecsharp
Experiment 3
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Menopause Change of Life, Female,Menopause,menopause
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peri/postmenopausal women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Urine samples from patients with peri/postmenopausal menopausal status from the entire cohort, consisting of both cancer and healthy patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- 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
- increased
Signature 1
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum
Abundance in Group 1: increased abundance in Peri/postmenopausal women
Revision editor(s): Ecsharp
Signature 2
Source: Supplementary Table 4: B) Urine
Description: Taxa Significantly Different in Premenopausal vs. Peri/Postmenopausal Patient Samples by Wilcoxon Rank Sum
Abundance in Group 1: decreased abundance in Peri/postmenopausal women
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillaceae | ||
| Shuttleworthella | ||
| Lactobacillales | ||
| Bacilli | ||
| Bacillota |
Revision editor(s): Ecsharp
Retrieved from "https://bugsigdb.org/w/index.php?title=29152146&oldid=206675"
