Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36631533

DOI Digital object identifier for electronic documents.

10.1038/s41598-023-27436-3

URI

Authors

Shrode RL, Knobbe JE, Cady N, Yadav M, Hoang J, Cherwin C, Curry M, Garje R, Vikas P, Sugg S, Phadke S, Filardo E, Mangalam AK

Journal

Scientific reports

Year

2023

As geographical location can impact the gut microbiome, it is important to study region-specific microbiome signatures of various diseases. Therefore, we profiled the gut microbiome of breast cancer (BC) patients of the Midwestern region of the United States. The bacterial component of the gut microbiome was profiled utilizing 16S ribosomal RNA sequencing. Additionally, a gene pathway analysis was performed to assess the functional capabilities of the bacterial microbiome. Alpha diversity was not significantly different between BC and healthy controls (HC), however beta diversity revealed distinct clustering between the two groups at the species and genera level. Wilcoxon Rank Sum test revealed modulation of several gut bacteria in BC specifically reduced abundance of those linked with beneficial effects such as Faecalibacterium prausnitzii. Machine learning analysis confirmed the significance of several of the modulated bacteria found by the univariate analysis. The functional analysis showed a decreased abundance of SCFA (propionate) production in BC compared to HC. In conclusion, we observed gut dysbiosis in BC with the depletion of SCFA-producing gut bacteria suggesting their role in the pathobiology of breast cancer. Mechanistic understanding of gut bacterial dysbiosis in breast cancer could lead to refined prevention and treatment.

Experiment 1

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Curated date: 2023/10/03

Curator: ChiomaBlessing

Revision editor(s): 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: 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

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls (HC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: breast cancer (BC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All BC patients eligible for this study were diagnosed with invasive BC of any stage, and recruited from the Breast Molecular Epidemiology Resource (BMER) of the Holden Comprehensive Cancer Center (HCCC)

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: 22

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Participants who were currently on antibiotics during 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): 0.05

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: body mass index, race, sex

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

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Source: Figure 3

Description: Taxonomic differences between the fecal microbiota of patients with BC and HC

Abundance in Group 1: increased abundance in breast cancer (BC)

NCBI	Quality Control	Links
Actinomyces
Blautia
Eggerthella
Faecalitalea
Intestinibacter bartlettii
Oscillospiraceae

Revision editor(s): ChiomaBlessing

Signature 2

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Curated date: 2023/10/03

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 4

Description: Taxonomic differences between the fecal microbiota of patients with BC and HC

Abundance in Group 1: decreased abundance in breast cancer (BC)

NCBI	Quality Control	Links
Alistipes sp.
Faecalibacterium prausnitzii
Lachnoclostridium edouardi
Lachnospira pectinoschiza
Oscillibacter sp.
Parabacteroides merdae
uncultured Erysipelotrichaceae bacterium
uncultured Lachnospiraceae bacterium

Revision editor(s): ChiomaBlessing