Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Subjects

Location of subjects: Germany; 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: Physical activity Activities, Locomotor,Activities, Motor,Activities, Physical,Activity, Locomotor,Activity, Motor,Activity, Physical,Locomotor Activities,Locomotor Activity,Motor Activities,Motor Activity,Physical Activities,Physical activity,physical activity

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients that are not engaged in any regular physical activity or exercise.

Group 0 sample size Number of subjects in the control (unexposed) group: 72

Group 1 sample size Number of subjects in the case (exposed) group: 107

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

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: Wald Test

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: sex, Confounders controlled for: "neoadjuvant treatment" 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.neoadjuvant treatment, Confounders controlled for: "stage at diagnosis" 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.stage at diagnosis, Confounders controlled for: "study site" 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.study site

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Source: Supplementary Table 2

Description: Differential abundance (mean normalized counts) at phylum level inactive group VS active group

Abundance in Group 1: increased abundance in Inactive patients

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Actinomycetota

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Source: Table 2

Description: Differential abundance (mean normalized counts) at genus level in inactive group VS active group

Abundance in Group 1: decreased abundance in Inactive patients

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Succinivibrio
Succiniclasticum

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/14

Curator: Deacme

Revision editor(s): Atrayees, Deacme, ChiomaBlessing

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: Normal weight patients

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patient with a BMI greater than or equal to 25 kg/m2 but not greater than 30 kg/m2.

Group 0 sample size Number of subjects in the control (unexposed) group: 59

Group 1 sample size Number of subjects in the case (exposed) group: 76

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: sex, Confounders controlled for: "study site" 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.study site, Confounders controlled for: "neoadjuvant treatment" 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.neoadjuvant treatment, Confounders controlled for: "stage at diagnosis" 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.stage at diagnosis

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Source: Table 2

Description: Differential abundance (mean normalized counts) at genus level in overweight group VS normal weight group

Abundance in Group 1: decreased abundance in Overweight patients

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Olsenella
unclassified Mogibacterium
Anaerococcus
Eubacterium
Clostridium
Succiniclasticum
Succinivibrio

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, ChiomaBlessing

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with a BMI greater than 30 kg/m2

Group 1 sample size Number of subjects in the case (exposed) group: 44

Lab analysis

Statistical Analysis

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Source: Table 2

Description: Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group

Abundance in Group 1: increased abundance in Obese patients

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Ruminococcus

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-1

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Source: Table 2

Description: Differential abundance (mean normalized counts) at genus level in obese group VS normal weight group

Abundance in Group 1: decreased abundance in Obese patients

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Adlercreutzia
Clostridium
Succinivibrio

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Body mass index , Physical activity BMI,Quetelet's Index,Body mass index,body mass index,Activities, Locomotor,Activities, Motor,Activities, Physical,Activity, Locomotor,Activity, Motor,Activity, Physical,Locomotor Activities,Locomotor Activity,Motor Activities,Motor Activity,Physical Activities,Physical activity,physical activity

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Normal weight/active patients

Group 1 name Corresponds to the case (exposed) group for case-control studies: Normal weight/inactive patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.

Group 0 sample size Number of subjects in the control (unexposed) group: 26

Group 1 sample size Number of subjects in the case (exposed) group: 33

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: sex, Confounders controlled for: "stage at diagnosis" 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.stage at diagnosis, Confounders controlled for: "neoadjuvant treatment" 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.neoadjuvant treatment, Confounders controlled for: "study site" 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.study site

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-4

Curated date: 2024/02/04

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Table 3

Description: Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group

Abundance in Group 1: decreased abundance in Normal weight/inactive patients

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Succiniclasticum
Succinivibrio

Revision editor(s): ChiomaBlessing

Signature 2

Mark reviewed

Needs review

Curated date: 2024/02/04

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Table 3

Description: Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group

Abundance in Group 1: increased abundance in Normal weight/inactive patients

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Pyramidobacter

Revision editor(s): ChiomaBlessing

Experiment 5

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Overweight/Obese/active patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patient with a BMI greater than or equal to 25 kg/m2 but is also physically active.

Group 1 sample size Number of subjects in the case (exposed) group: 46

Lab analysis

Statistical Analysis

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-4

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Source: Table 3

Description: Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in overweight/ obese active group compared to normal weight active group

Abundance in Group 1: increased abundance in Overweight/Obese/active patients

NCBI	Quality Control	Links
Pyramidobacter

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Source: Table 3 & Supplementary Table 3

Description: Differential abundance (mean normalized counts) at genus and phylum level (by individual BMI and physical activity groups) in overweight/ obese active group compared to normal weight active group

Abundance in Group 1: decreased abundance in Overweight/Obese/active patients

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Fusobacteriia
Peptoniphilus
Succiniclasticum
Succinivibrio

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: Overweight/Obese/inactive patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patient with a BMI equal to or greater than 25 kg/m2 and is physically inactive.

Group 1 sample size Number of subjects in the case (exposed) group: 74

Lab analysis

Statistical Analysis

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Source: Supplementary Table 3

Description: Differential abundances (mean normalized counts) at phylum level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group

Abundance in Group 1: increased abundance in Overweight/Obese/inactive patients

NCBI	Quality Control	Links
Actinomycetota

Revision editor(s): Atrayees, Deacme, Aiyshaaaa, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-4

Curated date: 2024/02/04

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Table 3

Description: Differential abundances (mean normalized counts) at genus level (by combined BMI and physical activity groups) in overweight/ obese/ inactive group VS normal weight/ active group

Abundance in Group 1: decreased abundance in Overweight/Obese/inactive patients

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Succinivibrio
RFN20RFN20

Revision editor(s): ChiomaBlessing

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3

Curated date: 2023/03/16

Curator: Deacme

Revision editor(s): Deacme, Atrayees, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Overweight/Obese/active patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with BMI greater than or equal to 25 kg/m2 and are not physically active.

Group 0 sample size Number of subjects in the control (unexposed) group: 46

Lab analysis

Statistical Analysis

Alpha Diversity

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

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

Richness Number of species: decreased

Signature 1