Comparative analysis of racial differences in breast tumor microbiome

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/22

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Victoria

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: Neoplasm cell process disease,disease of cellular proliferation,neoplasia,neoplasm,neoplasm (disease),neoplastic disease,neoplastic growth,other neoplasm,tumor,tumor disease,Neoplasm

Group 0 name Corresponds to the control (unexposed) group for case-control studies: BNH with TNBC normal tissue

Group 1 name Corresponds to the case (exposed) group for case-control studies: BNH with TNBC tumor tissue

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Tumor tissue from black non-hispanic patients with triple negative breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 7

Group 1 sample size Number of subjects in the case (exposed) group: 7

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.

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)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): Chloe, Itslanapark

Source: Figure 6a

Description: Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.

Abundance in Group 1: decreased abundance in BNH with TNBC tumor tissue

NCBI	Quality Control	Links
Actinomycetota
unclassified Bradyrhizobiaceae

Revision editor(s): Chloe, Itslanapark

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/22

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: WNH with TNBC normal tissue

Group 1 name Corresponds to the case (exposed) group for case-control studies: WNH with TNBC normal tissue

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Tumor tissue from white non-hispanic patients with triple negative breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 6

Group 1 sample size Number of subjects in the case (exposed) group: 6

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 6

Description: Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.

Abundance in Group 1: increased abundance in WNH with TNBC normal tissue

NCBI	Quality Control	Links
Bacteroidota

Revision editor(s): Itslanapark

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/22

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: WNH with TNBC normal tissue (second set)

Group 1 name Corresponds to the case (exposed) group for case-control studies: WNH with TNBC normal tissue (second set)

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Richness Number of species: increased

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/22

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: TPBC normal tissue

Group 1 name Corresponds to the case (exposed) group for case-control studies: TPBC tumor tissue

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Tumor tissue from patients with triple positive breast cancer

Lab analysis

Statistical Analysis

Alpha Diversity

Chao1 Abundance-based estimator of species richness: increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Table 6

Description: Microbiota relative abundance at phylum (a, b, d) and genus (c,e) levels showed differences between tumor and normal tissue in both triple negative breast cancer and triple positive breast cancer patients using Wilcoxon Signed Rank Test.

Abundance in Group 1: increased abundance in TPBC tumor tissue

NCBI	Quality Control	Links
Fusobacteriota
Streptococcus

Revision editor(s): Itslanapark

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): WikiWorks, LGeistlinger, Chloe, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Ethnic group Ethnicity,race,Ethnic group,ethnic group

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Normal tissue from black non-hispanic patients with breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group: 6

Group 1 sample size Number of subjects in the case (exposed) group: 7

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 8

Description: Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.

Abundance in Group 1: increased abundance in BNH

NCBI	Quality Control	Links
Planococcaceae

Revision editor(s): Itslanapark

Signature 2

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 8

Description: Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.

Abundance in Group 1: decreased abundance in BNH

NCBI	Quality Control	Links
Phenylobacterium

Revision editor(s): Itslanapark

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/26

Curator: Itslanapark

Revision editor(s): WikiWorks, LGeistlinger, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Tumor tissue from black non-hispanic patients with breast cancer

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: decreased

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/27

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Figure 8

Description: Relative abundance of taxa showed differences between BNH and WNH at the genus (a, b) and phylum (c) levels in TNBC (a, c) and TPBC (b) patients, significance analyzed using a Wilcoxon Rank Sum Test.

Abundance in Group 1: increased abundance in BNH

NCBI	Quality Control	Links
Veillonella
Phyllobacterium

Revision editor(s): Itslanapark

Signature 2