Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study/Experiment 5

From BugSigDB


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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): LGeistlinger, Itslanapark, 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
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
Grade Low (I/II)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Grade High (III)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
breast cancer patients with grade high level tumors (Grade III)
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
23
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: 2021/07/07

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Table 4

Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.

Abundance in Group 1: increased abundance in Grade High (III)

NCBI Quality ControlLinks
Eggerthella

Revision editor(s): Itslanapark

Signature 2

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Table 4

Description: Mean estimate ratios found using zero- inflated negative binomial model of taxa abundances by grade and stage of breast cancer.

Abundance in Group 1: decreased abundance in Grade High (III)

NCBI Quality ControlLinks
Lachnospiraceae
Anaerostipes

Revision editor(s): Itslanapark