Gut microbiome mediates the associations between lifestyle factors and risk of colorectal high-risk adenoma: results from a population-based cohort study
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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
- China
- 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
- Colorectal cancer 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,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-risk adenomas
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have colorectal cancer with high-risk adenomas
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1253
- Group 1 sample size Number of subjects in the case (exposed) group
- 272
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- log transformation
- Statistical test
- MaAsLin2
- 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
- age, alcohol consumption measurement, family history of cancer, polyp, smoking behavior, Confounders controlled for: "NSAIDs 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.NSAIDs use, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "recruitment region of participants" 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.recruitment region of participants, sex
Signature 1
Source: Figure 3A
Description: Analysis of the differential microbiota between high-risk adenomas (HRA) and control group
Abundance in Group 1: increased abundance in High-risk adenomas
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium | ||
Gemella | ||
Tyzzerella 4Tyzzerella 4 |
Revision editor(s): Temmie
Signature 2
Source: Figure 3A
Description: Analysis of the differential microbiota between high-risk adenomas (HRA) and control group
Abundance in Group 1: decreased abundance in High-risk adenomas
NCBI | Quality Control | Links |
---|---|---|
Pediococcus | ||
Proteus | ||
Pseudomonas | ||
Staphylococcus | ||
Lachnospiraceae UCG 004Lachnospiraceae UCG 004 | ||
Lachnospiraceae UCG 003Lachnospiraceae UCG 003 |
Revision editor(s): Temmie
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alcohol consumption measurement Alcohol consumption measurement,alcohol consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Alcohol Consumption
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Alcohol Consumption
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high levels of alcohol consumption
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, family history of cancer, polyp, Confounders controlled for: "NSAID 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.NSAID use, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "recruitment region of participants" 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.recruitment region of participants, sex
Signature 1
Source: Figure 2A
Description: Association between the gut genera and the lifestyle factor (alcohol consumption) in the Chinese Cohort
Abundance in Group 1: increased abundance in High Alcohol Consumption
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium | ||
Holdemanella | ||
Megamonas | ||
Negativibacillus | ||
Slackia | ||
Prevotella 9Prevotella 9 | ||
Tyzzerella 3Tyzzerella 3 | ||
Clostridium |
Revision editor(s): Temmie
Signature 2
Source: Figure 2A
Description: Association between the gut genera and the lifestyle factor (alcohol consumption) in the Chinese Cohort
Abundance in Group 1: decreased abundance in High Alcohol Consumption
Revision editor(s): Temmie
Experiment 3
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
- Low Body mass index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Body mass index
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high body mass index
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, family history of cancer, polyp, sex, Confounders controlled for: "NSAID 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.NSAID use, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "recruitment region of participants" 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.recruitment region of participants
Signature 1
Source: Figure 2A
Description: Association between gut genera and lifestyle risk factor (body mass index) in the Chinese cohort
Abundance in Group 1: increased abundance in High Body mass index
NCBI | Quality Control | Links |
---|---|---|
Allisonella | ||
Megamonas | ||
Agathobacter | ||
Collinsella | ||
Weissella | ||
Tyzzerella 3Tyzzerella 3 |
Revision editor(s): Temmie
Signature 2
Source: Figure 2A
Description: Association between gut genera and lifestyle risk factor (body mass index) in the Chinese cohort
Abundance in Group 1: decreased abundance in High Body mass index
Revision editor(s): Temmie
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking status measurement Smoking status measurement,smoking status measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Cigarette consumption
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Cigarette consumption
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with a high level of cigarette consumption
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol consumption measurement, family history of cancer, polyp, smoking behavior, Confounders controlled for: "NSAIDs 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.NSAIDs use, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "recruitment region of participants" 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.recruitment region of participants, sex
Signature 1
Source: Figure 2A
Description: Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the Chinese cohort
Abundance in Group 1: increased abundance in High Cigarette consumption
NCBI | Quality Control | Links |
---|---|---|
Actinomyces | ||
Bilophila | ||
Mediterraneibacter gnavus |
Revision editor(s): Temmie
Signature 2
Source: Figure 2A
Description: Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the Chinese cohort
Abundance in Group 1: decreased abundance in High Cigarette consumption
NCBI | Quality Control | Links |
---|---|---|
Haemophilus | ||
Lachnospiraceae UCG 003Lachnospiraceae UCG 003 |
Revision editor(s): Temmie
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alcohol consumption measurement Alcohol consumption measurement,alcohol consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Alcohol Consumption (Japanese cohort)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Alcohol Consumption (Japanese cohort)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high levels of alcohol consumption in the Japanese cohort
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol consumption measurement, body mass index, sex, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "Brinkman index of smoking" 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.Brinkman index of smoking
Signature 1
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (ALCOHOL CONSUMPTION) in the EXTERNAL Japanese cohort
Abundance in Group 1: increased abundance in High Alcohol Consumption (Japanese cohort)
NCBI | Quality Control | Links |
---|---|---|
Allisonella | ||
Megamonas | ||
Megasphaera | ||
Paratractidigestivibacter | ||
Fusobacterium | ||
Intestinibacillus |
Revision editor(s): Temmie
Signature 2
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (ALCOHOL CONSUMPTION) in the external Japanese cohort
Abundance in Group 1: decreased abundance in High Alcohol Consumption (Japanese cohort)
NCBI | Quality Control | Links |
---|---|---|
Dialister | ||
Faecalibacterium | ||
Bifidobacterium |
Revision editor(s): Temmie
Experiment 6
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
- Low Body mass index (Japanese cohort)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Body mass index (Japanese cohort)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high body mass index in the Japanese cohort
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, Confounders controlled for: "disease status" 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.disease status, Confounders controlled for: "Brinkman index of smoking" 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.Brinkman index of smoking, sex, alcohol consumption measurement
Signature 1
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (BODY MASS INDEX) in the EXTERNAL Japanese cohort.
Abundance in Group 1: increased abundance in High Body mass index (Japanese cohort)
NCBI | Quality Control | Links |
---|---|---|
Acidaminococcus | ||
Allisonella | ||
Fusobacterium | ||
unclassified Clostridium | ||
Granulicatella |
Revision editor(s): Temmie
Signature 2
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (BODY MASS INDEX) based on an EXTERNAL Japanese cohort
Abundance in Group 1: decreased abundance in High Body mass index (Japanese cohort)
Revision editor(s): Temmie
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking status measurement Smoking status measurement,smoking status measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Cigarette consumption (Japanese cohort)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Cigarette consumption (Japanese cohort)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high levels of cigarette consumption in the Japanese Cohort
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the EXTERNAL Japanese c\ohort
Abundance in Group 1: increased abundance in Low Cigarette consumption (Japanese cohort)
NCBI | Quality Control | Links |
---|---|---|
Brachyspira | ||
Solibaculum | ||
unclassified Erysipelotrichaceae |
Revision editor(s): Temmie
Signature 2
Source: Figure 2B
Description: Association between gut genera and lifestyle risk factor (CIGARETTE CONSUMPTION) in the EXTERNAL Japanese cohort
Abundance in Group 1: decreased abundance in Low Cigarette consumption (Japanese cohort)
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium | ||
Lacrimispora | ||
Merdimmobilis |
Revision editor(s): Temmie
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal cancer 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,Colorectal cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-risk adenomas
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who have high-risk adenomas
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1253
- Group 1 sample size Number of subjects in the case (exposed) group
- 272
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Figure 3B
Description: LefSe analysis of the differences in genera in the high-risk adenoma group and control group
Abundance in Group 1: increased abundance in High-risk adenomas
NCBI | Quality Control | Links |
---|---|---|
Actinomyces | ||
Fusobacterium | ||
Gemella | ||
Phascolarctobacterium | ||
Terrisporobacter | ||
Tyzzerella 4Tyzzerella 4 | ||
Ruminococcaceae UCG-004Ruminococcaceae UCG-004 |
Revision editor(s): Temmie
Signature 2
Source: Figure 3B
Description: LefSe analysis of the differences in genera between the high-risk adenoma group and the control group
Abundance in Group 1: decreased abundance in High-risk adenomas
NCBI | Quality Control | Links |
---|---|---|
Dialister | ||
Faecalibacterium | ||
Lachnospira | ||
Oscillibacter | ||
Parasutterella | ||
Lachnospiraceae UCG-004Lachnospiraceae UCG-004 | ||
Ruminococcaceae UCG-003Ruminococcaceae UCG-003 | ||
Prevotellaceae |
Revision editor(s): Temmie