Gut mucosal microbiome across stages of colorectal carcinogenesis
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2022/06/24
Curator: Jeshudy
Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Peace Sandy
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
- Intestine Bowel,Intestinal tract,Intestine,intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histology-proven adenoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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)?
- Yes
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between patients with colorectal adenoma and controls
Abundance in Group 1: increased abundance in colorectal adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacteroides uniformis | ||
| Blautia sp. | ||
| Enhydrobacter sp. | ||
| Escherichia coli | ||
| Gemella sp. | ||
| Parvimonas sp. | ||
| Peptostreptococcus sp. | ||
| Prevotella intermedia |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplementary Figure 9
Description: Differential microbial abundance between patients with colorectal adenoma and controls
Abundance in Group 1: decreased abundance in colorectal adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacteroides sp. | ||
| Bacteroides uniformis | ||
| Blautia obeum | ||
| Blautia sp. | ||
| Coprococcus sp. | ||
| Faecalibacterium prausnitzii | ||
| Prevotella sp. |
Revision editor(s): Jeshudy, Claregrieve1
Experiment 2
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 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer (adenocarcinoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with invasive adenocarcinoma
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplemental Figure 9
Description: Differential microbial abundance between patients with colorectal adenocarcinoma and controls
Abundance in Group 1: increased abundance in colorectal cancer (adenocarcinoma)
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplemental Figure 9
Description: Differential microbial abundance between patients with colorectal adenocarcinoma and controls
Abundance in Group 1: decreased abundance in colorectal cancer (adenocarcinoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. | ||
| Blautia sp. | ||
| Escherichia coli | ||
| Faecalibacterium prausnitzii | ||
| Pseudomonas veronii |
Revision editor(s): Jeshudy, Claregrieve1
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal adenoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma
Abundance in Group 1: increased abundance in colorectal cancer
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplemental Figure 9
Description: Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma
Abundance in Group 1: decreased abundance in colorectal cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Enhydrobacter sp. | ||
| Escherichia coli | ||
| Pedobacter cryoconitis | ||
| Pseudomonas veronii | ||
| Rothia terrae |
Revision editor(s): Jeshudy, Claregrieve1
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- carcinoma-adjacent mucosae
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- carcinoma mucosae
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- specimens collected from adenocarcinoma tissue
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "subject" 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.subject
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae
Abundance in Group 1: decreased abundance in carcinoma mucosae
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia sp. | ||
| Pseudomonas veronii |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplemental Figure 9
Description: Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae
Abundance in Group 1: increased abundance in carcinoma mucosae
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium sp. |
Revision editor(s): Jeshudy, Claregrieve1
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- adenoma-adjacent
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenocarcinoma mucosae
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples
Abundance in Group 1: decreased abundance in adenocarcinoma mucosae
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus sp. (in: firmicutes) | ||
| Enhydrobacter sp. | ||
| Escherichia coli | ||
| Pedobacter cryoconitis | ||
| Pseudomonas veronii | ||
| Rothia terrae |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples
Abundance in Group 1: increased abundance in adenocarcinoma mucosae
Revision editor(s): Jeshudy, Claregrieve1
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenoma-adjacent
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- specimen collected adjacent to histology-proven adenoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue
Abundance in Group 1: decreased abundance in adenoma-adjacent
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia sp. | ||
| Coprococcus sp. | ||
| Enterocloster clostridioformis | ||
| Faecalibacterium prausnitzii |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplemental Figure 9
Description: Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue
Abundance in Group 1: increased abundance in adenoma-adjacent
| NCBI | Quality Control | Links |
|---|---|---|
| Enhydrobacter sp. | ||
| Fusobacterium sp. | ||
| Pedobacter cryoconitis |
Revision editor(s): Jeshudy, Claregrieve1
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 1 name Corresponds to the case (exposed) group for case-control studies
- carcinoma-adjacent
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- specimen collected from tissue adjacent to adenocarcinoma site
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
Statistical Analysis
Signature 1
Source: Supplemental Figure 9
Description: Differential microbial abundance between healthy control tissue and adenocarcinoma-adjacent tissue
Abundance in Group 1: increased abundance in carcinoma-adjacent
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Bacteroides ovatus | ||
| Fusobacterium sp. | ||
| Gemella sp. | ||
| Granulicatella sp. | ||
| Peptostreptococcus sp. | ||
| Porphyromonas endodontalis | ||
| Prevotella sp. |
Revision editor(s): Jeshudy, Claregrieve1
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- colorectal adenoma tissue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- carcinoma-adjacent tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- specimens collected from tissue adjacent to adenocarcinoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- 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
Signature 1
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples
Abundance in Group 1: increased abundance in carcinoma-adjacent tissue
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Source: Supplementary Figure 9
Description: Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples
Abundance in Group 1: decreased abundance in carcinoma-adjacent tissue
| NCBI | Quality Control | Links |
|---|---|---|
| Enhydrobacter sp. |
Revision editor(s): Jeshudy, Claregrieve1
