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

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

Curated date: 2021/06/21

Curator: Itslanapark

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Itslanapark, Peace Sandy

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: HER2 Positive Breast Carcinoma ERBB2 Overexpressing subtype of breast carcinoma,HER2 Overexpressing breast carcinoma,HER2 Overexpressing subtype of breast carcinoma,HER2 Positive breast cancer,HER2 positive breast carcinoma,Her2-receptor positive breast cancer,HER2 Positive Breast Carcinoma,hER2 Positive Breast Carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Her2 negative tumor

Group 1 name Corresponds to the case (exposed) group for case-control studies: Her2 positive tumor

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients with Her2 positive tumors (human epidermal growth factor receptive 2 positive)

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 12

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

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): 0.001

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: 2021/06/29

Curator: Itslanapark

Revision editor(s): Itslanapark

Source: Table 3

Description: Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by HER2 status

Abundance in Group 1: increased abundance in Her2 positive tumor

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Acidaminococcus

Revision editor(s): Itslanapark

Signature 2

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

Curated date: 2021/06/30

Curator: Itslanapark

Revision editor(s): Itslanapark, Claregrieve1

Source: Table 3

Description: Mean ratio estimates found using zero-inflated negative binomial model of taxa abundance by ER, PR, and HER2 status

Abundance in Group 1: decreased abundance in Her2 positive tumor

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Desulfovibrio
Ruminococcus
Christensenellaceae

Revision editor(s): Itslanapark, Claregrieve1

Experiment 2

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

Curated date: 2021/07/05

Curator: Itslanapark

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

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Age at menarche Age at menarche,age at menarche

Group 0 name Corresponds to the control (unexposed) group for case-control studies: early age at menarche (≤11)

Group 1 name Corresponds to the case (exposed) group for case-control studies: later age at menarche (≥12)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: breast cancer patients with age at menarche being over 12 years old

Group 0 sample size Number of subjects in the control (unexposed) group: 11

Group 1 sample size Number of subjects in the case (exposed) group: 26

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: increased

Signature 1

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): Itslanapark, Claregrieve1

Source: Table 5

Description: Mean estimate ratios gound using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.

Abundance in Group 1: increased abundance in later age at menarche (≥12)

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Escherichia

Revision editor(s): Itslanapark, Claregrieve1

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 5

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.

Abundance in Group 1: decreased abundance in later age at menarche (≥12)

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Methanobrevibacter
Ruminococcus

Revision editor(s): Itslanapark

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): WikiWorks, LGeistlinger, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

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

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

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-

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Haemophilus
Veillonella

Revision editor(s): Itslanapark

Experiment 5

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

Curated date: 2021/07/07

Curator: Itslanapark

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

Differences from previous experiment shown

Subjects

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

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

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)

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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)

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Lachnospiraceae
Anaerostipes

Revision editor(s): Itslanapark

Experiment 6

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Breast cancer stage Breast cancer stage,breast cancer stage

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Stage Low (I/II)

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients with high stage progression of breast cancer (Stage III).

Group 0 sample size Number of subjects in the control (unexposed) group: 22

Group 1 sample size Number of subjects in the case (exposed) group: 15

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

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 Stage High (III)

NCBI	Quality Control	Links
Clostridium
Veillonella
Haemophilus

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 Stage High (III)

NCBI	Quality Control	Links
Acidaminococcus
Catenibacterium

Revision editor(s): Itslanapark

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Age Age,age

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Age 50+

Group 1 name Corresponds to the case (exposed) group for case-control studies: Age ≤50

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients whose age is ≤50 years old.

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 20

Lab analysis

Statistical Analysis

Statistical test: Kruskall-Wallis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: 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 5

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.

Abundance in Group 1: increased abundance in Age ≤50

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Clostridiaceae
Clostridium
Enterobacteriaceae
Lactococcus

Revision editor(s): Itslanapark

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Parous Parous,parous

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients who are nulliparous (have had no live births.)

Group 0 sample size Number of subjects in the control (unexposed) group: 29

Group 1 sample size Number of subjects in the case (exposed) group: 8

Lab analysis

Statistical Analysis

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 5

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by age group, menarche age and parity.

Abundance in Group 1: decreased abundance in Nulliparous

NCBI	Quality Control	Links
Catenibacterium

Revision editor(s): Itslanapark

Experiment 9

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Body mass index BMI,Quetelet's Index,Body mass index,body mass index

Group 0 name Corresponds to the control (unexposed) group for case-control studies: BMI<25

Group 1 name Corresponds to the case (exposed) group for case-control studies: BMI≥25

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients with a high body mass index (BMI≥25)

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

Lab analysis

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

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 6

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.

Abundance in Group 1: increased abundance in BMI≥25

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Akkermansia

Revision editor(s): Itslanapark

Experiment 10

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

Curated date: 2021/07/07

Curator: Itslanapark

Revision editor(s): WikiWorks, Claregrieve1, Itslanapark, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Body fat percentage Body fat percentage,body fat percentage

Group 0 name Corresponds to the control (unexposed) group for case-control studies: TBF≤46%

Group 1 name Corresponds to the case (exposed) group for case-control studies: TBF>46%

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Breast cancer patients with a total body fat percentage ≥46%.

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 12

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Not specified

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

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 6

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.

Abundance in Group 1: increased abundance in TBF>46%

NCBI	Quality Control	Links
Clostridiaceae

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 6

Description: Mean estimate ratios found using a zero-inflated negative binomial model of taxa abundances by BMI, total body fat, and physical activity.

Abundance in Group 1: decreased abundance in TBF>46%

NCBI	Quality Control	Links
Coriobacteriaceae

Revision editor(s): Itslanapark

Experiment 11