Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Germany
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- colorectal cancer , physical activity cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Activities, Locomotor,Activities, Motor,Activities, Physical,Activity, Locomotor,Activity, Motor,Activity, Physical,Locomotor Activities,Locomotor Activity,Motor Activities,Motor Activity,Physical Activities,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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- body mass index, physical activity, race, sex, smoking status, Matched on: "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, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "aspirin use" 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.aspirin use, ethnic group
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
Signature 1
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Inactive patients
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Fusobacteriia | ||
Pseudomonadota | ||
Synergistota |
Signature 2
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physical activity groups
Abundance in Group 1: decreased abundance in Inactive patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Verrucomicrobiae | ||
Mycoplasmatota | ||
Bacteroidia |
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- colorectal cancer , body mass index cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,BMI,Quetelet's 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, race, sex, smoking status, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "neo adjuvant 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.neo adjuvant treatment, Matched on: "aspirin use" 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.aspirin use, ethnic group
Signature 1
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Overweight patients
NCBI | Quality Control | Links |
---|---|---|
Actinomycetota | ||
Bacillota | ||
Bacteroidia | ||
Verrucomicrobiae |
Signature 2
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: decreased abundance in Overweight patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Fusobacteriia | ||
Mycoplasmatota | ||
Pseudomonadota | ||
Synergistota |
Experiment 3
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, physical activity, race, sex, smoking status, Matched on: "ethnicity" 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.ethnicity, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "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, Matched on: "aspirin use" 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.aspirin use
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
Signature 1
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Obese patients
NCBI | Quality Control | Links |
---|---|---|
Fusobacteriia | ||
Actinomycetota | ||
Pseudomonadota | ||
Bacteroidia |
Signature 2
Source: Supplementary Table 2
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: decreased abundance in Obese patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Verrucomicrobiota | ||
Synergistota | ||
Bacillota | ||
Mycoplasmatota |
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- colorectal cancer , body mass index , physical activity cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,BMI,Quetelet's 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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, physical activity, race, sex, smoking status, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "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, Matched on: "aspirin use" 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.aspirin use, ethnic group
Signature 1
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by combined BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Normal weight/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Actinomycetota | ||
Bacillota | ||
Mycoplasmatota | ||
Synergistota | ||
Verrucomicrobiae |
Signature 2
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: decreased abundance in Normal weight/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Fusobacteriia | ||
Bacteroidia |
Experiment 5
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, physical activity, race, sex, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "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, Matched on: "aspirin use" 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.aspirin use, ethnic group, smoking status
Signature 1
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Overweight/Obese/active patients
NCBI | Quality Control | Links |
---|---|---|
Verrucomicrobiae | ||
Bacteroidia | ||
Mycoplasmatota | ||
Bacillota | ||
Actinomycetota | ||
Synergistota |
Signature 2
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: decreased abundance in Overweight/Obese/active patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Fusobacteriia | ||
Pseudomonadota |
Experiment 6
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, physical activity, race, sex, smoking status, Matched on: "stage at diagnos" 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 diagnos, Matched on: "tumor 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.tumor site, Matched on: "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, Matched on: "aspirin use" 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.aspirin use, ethnic group
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table 3
Description: Differential abundances (mean normalized counts) at phylum level by com- bined BMI and physical activity groups
Abundance in Group 1: increased abundance in Overweight/Obese/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Verrucomicrobiae | ||
Bacillota | ||
Synergistota | ||
Bacteroidia | ||
Actinomycetota | ||
Pseudomonadota |
Signature 2
Source: Supplementary Table 3
Description: Differential abundances (mean normalized counts) at phylum level by com- bined BMI and physical activity groups
Abundance in Group 1: decreased abundance in Overweight/Obese/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Fusobacteriia | ||
Mycoplasmatota |
Experiment 7
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, physical activity, race, sex, smoking status, Matched on: "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, Matched on: "tumor 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.tumor site, Matched on: "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, Matched on: "aspirin use" 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.aspirin use, ethnic group
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: increased abundance in Overweight/Obese/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Psychotria ramuensis | ||
Verrucomicrobiae | ||
Synergistota | ||
Cleisthenes | ||
Pseudomonadota | ||
Bacillota |
Signature 2
Source: Supplementary Table 3
Description: Differential abundance (mean normalized counts) at genus level by individual BMI and physi- cal activity groups
Abundance in Group 1: decreased abundance in Overweight/Obese/inactive patients
NCBI | Quality Control | Links |
---|---|---|
Cyanobacteriota | ||
Fusobacteriia | ||
Bacteroidia |