Urinary and oral microbiota in Polish women: a pilot case-control study of breast cancer

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

40330727

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2025.1538224

URI Uniform resource identifier for web resources.

Authors

Marciniak A, Skrzypczak-Zielińska M, Zakerska-Banaszak O, Nowakowska E, Kozaczka A, Zemła B, Szpak A, Godlewski D, Charzewska J, Pathak DR

Journal

Frontiers in microbiology

Year

2025

Keywords:

breast cancer, functional analysis, next-generation sequencing, oral microbiota, urinary microbiota

INTRODUCTION: The human microbiota can be a critical component in the development and progression of various diseases, including cancer. This study aims to investigate the composition of the urinary and oral microbiota in Polish breast cancer (BC) patients relative to healthy controls (HCs) and to predict relevant metabolic pathways of microbiota in studied groups. METHODS: Urine and oral samples from 48 participants, 24 BC cases and 24 HCs, randomly selected from 417 BC cases and 514 HCs, were analyzed using next-generation sequencing of bacterial 16S rRNA gene (V1-V9) and fungal ITS regions, along with bioinformatics tools to identify and compare microbial communities and predict relevant pathways of microbiota in the studied groups. RESULTS: BC case urine microbiota contained an increased abundance of Corynebacterium (5.2-fold, but not significant) and Gammaproteobacteria including unknown genus and Pseudomonas (1.7- and 1.8-fold) and decreased abundance of Family XI (0.3-fold) and Bifidobacteriaceae (0.4-fold) compared to HCs. Oral BC microbiota contains higher levels of the bacterial families P5D1-392, Leptotrichiaceae, and Pasteurellaceae (3.3-, 3.3-, and 1.9-fold, respectively), whereas the genera Cellulosimicrobium, Pseudomonas, and Pantoea were significantly less abundant (0.4-, 0.3-, and 0.3-fold, respectively). At the species level, the most differentiating species between BC and HC was uncultured Pseudomonas sp. (1.8-fold) in urine and Pantoea agglomerans (0.2-fold) in oral microbiota. Fungal composition did not show any significant differences between the groups. Functional analysis based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) predicted, e.g. enhanced hydrogen production and benzoyl-CoA degradation in BC cases, as well as reduced CMP-diacetamido-8-epilegionaminic acid biosynthesis. DISCUSSION: The study underscores the potential significance of the microbiota in BC pathogenesis. Further research is needed to elucidate the mechanisms underlying microbiota-tumor interactions and to explore the clinical applications.

Experiment 1

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Curated date: 2025/06/13

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Subjects

Location of subjects: Poland

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: Urine Urine,urine

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 (BC) cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: BC cases, regardless of subtype, with biological samples collected between 2004 and 2006 from 5 Regional Cancer Registries located in Poland

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: 24

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V9

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): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Matched on Factors on which subjects have been matched on in a case-control study: age, region of residence

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, menopause, smoking status, alcohol drinking

Alpha Diversity

Richness Number of species: unchanged

Signature 1

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Source: Figure 4

Description: Log 2 Fold changes of urine bacterial abundance between cases and healthy controls at different taxonomic levels

Abundance in Group 1: increased abundance in Breast cancer (BC) cases

NCBI	Quality Control	Links
Pseudomonadales
Pseudomonadaceae
unclassified Gammaproteobacteria
Pseudomonas
uncultured Pseudomonas sp.
uncultured Gammaproteobacteria bacterium

Revision editor(s): Ecsharp

Experiment 2

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, alcohol drinking, body mass index, menopause, smoking status

Alpha Diversity

Richness Number of species: unchanged

Signature 1

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Source: Figure 6

Description: Log 2 fold changes of oral wash bacterial abundance between cases and healthy controls at different taxonomic levels

Abundance in Group 1: decreased abundance in Breast cancer (BC) cases

NCBI	Quality Control	Links
Abiotrophia para-adiacens
Cellulosimicrobium cellulans LMG 16121
Pseudomonas sp.
Pantoea agglomerans
Cellulosimicrobium
Pseudomonas
Pantoea
Porphyromonadaceae
Pseudomonadaceae
Erwiniaceae
Pseudomonadales

Revision editor(s): Ecsharp