Microbiome composition indicate dysbiosis and lower richness in tumor breast tissues compared to healthy adjacent paired tissue, within the same women

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

34980006

DOI Digital object identifier for electronic documents.

10.1186/s12885-021-09074-y

URI Uniform resource identifier for web resources.

Authors

Esposito MV, Fosso B, Nunziato M, Casaburi G, D'Argenio V, Calabrese A, D'Aiuto M, Botti G, Pesole G, Salvatore F

Journal

BMC cancer

Year

2022

Keywords:

16S rRNA, Breast cancer microbiome, Breast cancer tissues, Breast healthy tissues, Microbial dysbiosis, Microbiome composition, Next generation sequencing, cancer/healthy paired samples

BACKGROUND: Breast cancer (BC) is the most common malignancy in women, in whom it reaches 20% of the total neoplasia incidence. Most BCs are considered sporadic and a number of factors, including familiarity, age, hormonal cycles and diet, have been reported to be BC risk factors. Also the gut microbiota plays a role in breast cancer development. In fact, its imbalance has been associated to various human diseases including cancer although a consequential cause-effect phenomenon has never been proven. METHODS: The aim of this work was to characterize the breast tissue microbiome in 34 women affected by BC using an NGS-based method, and analyzing the tumoral and the adjacent non-tumoral tissue of each patient. RESULTS: The healthy and tumor tissues differed in bacterial composition and richness: the number of Amplicon Sequence Variants (ASVs) was higher in healthy tissues than in tumor tissues (p = 0.001). Moreover, our analyses, able to investigate from phylum down to species taxa for each sample, revealed major differences in the two richest phyla, namely, Proteobacteria and Actinobacteria. Notably, the levels of Actinobacteria and Proteobacteria were, respectively, higher and lower in healthy with respect to tumor tissues. CONCLUSIONS: Our study provides information about the breast tissue microbial composition, as compared with very closely adjacent healthy tissue (paired samples within the same woman); the differences found are such to have possible diagnostic and therapeutic implications; further studies are necessary to clarify if the differences found in the breast tissue microbiome are simply an association or a concausative pathogenetic effect in BC. A comparison of different results on similar studies seems not to assess a universal microbiome signature, but single ones depending on the environmental cohorts' locations.

Experiment 1

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2025/06/10

Curator: Ecsharp

Revision editor(s): Ecsharp

Subjects

Location of subjects: Italy

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 adjacent paired tissue (H)

Group 1 name Corresponds to the case (exposed) group for case-control studies: tumor breast tissue (T)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Tumor breast tissue sample from women with unilateral breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 34

Group 1 sample size Number of subjects in the case (exposed) group: 34

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4-V6

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).: raw counts

Statistical test: DESeq2

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/06/10

Curator: Ecsharp

Revision editor(s): Ecsharp

Source: Table 3

Description: Taxa that differ significantly between healthy adjacent paired tissue and tumor breast tissue samples

Abundance in Group 1: increased abundance in tumor breast tissue (T)

NCBI	Quality Control	Links
Alphaproteobacteria
Pseudomonas brenneri
FirmicutesFirmicutes
Moraxella sp. S2

Revision editor(s): Ecsharp

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/06/10

Curator: Ecsharp

Revision editor(s): Ecsharp

Source: Table 3

Description: Taxa that differ significantly between healthy adjacent paired tissue and tumor breast tissue samples

Abundance in Group 1: decreased abundance in tumor breast tissue (T)

NCBI	Quality Control	Links
ActinobacteriaActinobacteria
Actinobacteria classActinobacteria class
Propionibacteriales
Aeromonadales
Selenomonadales
Propionibacteriaceae
Aeromonadaceae
Propionibacterium
Aeromonas
Variovorax sp. WO3
Pseudomonas sp. PS9(2007)
Propionibacterium sp. enrichment culture clone MRHull-FeSM-11E
Pseudomonas sp. IMER-A2-21
Neisseria elongata
Propionibacterium acnesPropionibacterium acnes

Revision editor(s): Ecsharp