Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study/Experiment 3

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31

Curated date: 2021/07/05

Curator: Itslanapark

Revision editor(s): Itslanapark, LGeistlinger, WikiWorks

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,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Estrogen receptor status Estrogen receptor status,estrogen receptor status
Group 0 name Corresponds to the control (unexposed) group for case-control studies
ER+
Group 1 name Corresponds to the case (exposed) group for case-control studies
ER-
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
breast cancer patients with negative Estrogen Receptor status
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
28
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Antibiotic use one week or more during the month prior to fecal 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

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.001
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, ethnic group, race, Confounders controlled for: "total counts" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.total counts

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31

Curated date: 2021/07/05

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Table 3

Description: Mean ratio estimates obtained by zero-inflated negative binomial model of taxa abundances by estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 status.

Abundance in Group 1: decreased abundance in ER-

NCBI Quality ControlLinks
Haemophilus
Veillonella

Revision editor(s): Itslanapark