Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Hoskinson C, Zheng K, Gabel J, Kump A, German R, Podicheti R, Marino N, Stiemsma LT
Journal
mSystems
Year
2022
Keywords:
16S, breast cancer, breast tissue, functional metagenome, microbiome, transcriptome
Microbiota studies have reported changes in the microbial composition of the breast upon cancer development. However, results are inconsistent and limited to the later phases of cancer development (after diagnosis). We analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H, n = 49) with those of tissues donated prior to (prediagnostic, PD, n = 15) and after (adjacent normal, AN, n = 49, and tumor, T, n = 46) breast cancer diagnosis (n total = 159). DNA was isolated from tissue samples and submitted for Illumina MiSeq paired-end sequencing of the V3-V4 region of the 16S gene. To infer bacterial function in breast cancer, we predicted the functional bacteriome from the 16S sequencing data using PICRUSt2. Bacterial compositional analysis revealed an intermediary taxonomic signature in the PD tissue relative to that of the H tissue, represented by shifts in Bacillaceae, Burkholderiaceae, Corynebacteriaceae, Streptococcaceae, and Staphylococcaceae. This compositional signature was enhanced in the AN and T tissues. We also identified significant metabolic reprogramming of the microbiota of the PD, AN, and T tissue compared with the H tissue. Further, preliminary correlation analysis between host transcriptome profiling and microbial taxa and genes in H and PD tissues identified altered associations between the human host and mammary microbiota in PD tissue compared with H tissue. These findings suggest that compositional shifts in bacterial abundance and metabolic reprogramming of the breast tissue microbiota are early events in breast cancer development that are potentially linked with cancer susceptibility. IMPORTANCE The goal of this study was to determine the role of resident breast tissue bacteria in breast cancer development. We analyzed breast tissue bacteria in healthy breast tissue and breast tissue donated prior to (precancerous) and after (postcancerous) breast cancer diagnosis. Compared to healthy tissue, the precancerous and postcancerous breast tissues demonstrated differences in the amounts of breast tissue bacteria. In addition, breast tissue bacteria exhibit different functions in pre-cancerous and post-cancerous breast tissues relative to healthy tissue. These differences in function are further emphasized by altered associations of the breast tissue bacteria with gene expression in the human host prior to cancer development. Collectively, these analyses identified shifts in bacterial abundance and metabolic function (dysbiosis) prior to breast tumor diagnosis. This dysbiosis may serve as a therapeutic target in breast cancer prevention.

Experiment 1


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, LGeistlinger, ChiomaBlessing

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 (H)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Prediagnostic (PD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples donated prior to breast cancer diagnosis
Group 0 sample size Number of subjects in the control (unexposed) group
49
Group 1 sample size Number of subjects in the case (exposed) group
15

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
LEfSe
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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3b

Description: Differentially abundant taxa in Prediagnostic group versus Healthy group

Abundance in Group 1: increased abundance in Prediagnostic (PD)

NCBI Quality ControlLinks
Caldimonas
Fusobacterium
Pantoea
Romboutsia
Sphingomonas
Staphylococcus
Streptococcus sp.

Revision editor(s): OdigiriGreat, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3b

Description: Differentially abundant taxa in Prediagnostic group versus Healthy group

Abundance in Group 1: decreased abundance in Prediagnostic (PD)

NCBI Quality ControlLinks
Corynebacterium

Revision editor(s): OdigiriGreat, ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, LGeistlinger, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Adjacent normal (AN)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
samples donated after breast cancer diagnosis (AN)
Group 1 sample size Number of subjects in the case (exposed) group
49

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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-9

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3c

Description: Differentially abundant taxa in Adjacent normal group versus Healthy group

Abundance in Group 1: increased abundance in Adjacent normal (AN)

NCBI Quality ControlLinks
Alcaligenes sp.
Anaerococcus
Atopostipes sp.
Corynebacterium
Duganella
Enterococcus sp.
Herbaspirillum sp.
Klebsiella
Oceanobacillus sp.
Proteus
Pseudogracilibacillus
Pseudomonas sp.
Tissierella sp.

Revision editor(s): OdigiriGreat, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3c

Description: Differentially abundant taxa in Adjacent normal group versus Healthy group

Abundance in Group 1: decreased abundance in Adjacent normal (AN)

NCBI Quality ControlLinks
Acinetobacter sp.
Arthrobacter
Bacteroides
Bradyrhizobium
Brochothrix
Carnobacterium sp.
Corynebacterium sp.
Cutibacterium
Iodobacter sp.
Lactococcus
Photobacterium
Pseudomonas sp.
Rubrobacter
Ruminococcus
Serratia
Staphylococcus sp.
Vagococcus

Revision editor(s): OdigiriGreat, ChiomaBlessing

Experiment 3


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, LGeistlinger, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Tumor (T)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Samples donated after breast cancer diagnosis (tumor)
Group 1 sample size Number of subjects in the case (exposed) group
46

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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3d

Description: Differentially abundant taxa in Tumor group versus Healthy group

Abundance in Group 1: increased abundance in Tumor (T)

NCBI Quality ControlLinks
Anaerococcus
Enterococcus sp.
Herbaspirillum sp.
Pseudogracilibacillus
Pseudomonas sp.
Rhodococcus
Staphylococcus sp.

Revision editor(s): OdigiriGreat, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/10/29

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, ChiomaBlessing

Source: Figure 3d

Description: Differentially abundant taxa in Tumor group versus Healthy group

Abundance in Group 1: decreased abundance in Tumor (T)

NCBI Quality ControlLinks
Acinetobacter
Arthrobacter
Bacteroides
Bilophila
Bradyrhizobium sp.
Brochothrix sp.
Carnobacterium sp.
Corynebacterium sp.
Iodobacter sp.
Lactococcus
Lawsonella
Muribaculaceae
Photobacterium
Pseudomonas sp.
Rubellimicrobium
Serratia
Staphylococcus sp.
Thermus
Vagococcus

Revision editor(s): OdigiriGreat, ChiomaBlessing

Experiment 4


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2024/01/10

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Prediagnostic (PD)
Group 0 sample size Number of subjects in the control (unexposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Experiment 5


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2024/01/10

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Adjacent Normal (AN)
Group 0 sample size Number of subjects in the control (unexposed) group
49

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged