Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer
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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.
- Mus musculus
- 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
- AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS to induce chronic colitis and colorectal cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- 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
- edgeR
- 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
Signature 1
Source: Table S2, Fig. 4B
Description: Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.
Abundance in Group 1: increased abundance in AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
Revision editor(s): Wendy640, KateRasheed
Signature 2
Source: Table S2, Fig. 4B
Description: Differential OTUs between control mice and AOM/DSS-treated mice, showing significant microbial shifts associated with colorectal cancer progression.
Abundance in Group 1: decreased abundance in AOS/DSS (Azoxymethane/Dextran Sodium Sulphate)-treated group
Revision editor(s): Wendy640, KateRasheed
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice with inflammation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice with dysplasia/cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that developed dysplasia and cancer and were treated with 3-4 AOM/DSS cycles
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S3
Description: OTUs distinguishing inflammation from colorectal cancer, highlighting taxa involved in cancer-related microbiome changes.
Abundance in Group 1: increased abundance in Mice with dysplasia/cancer
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Muribaculaceae |
Revision editor(s): Wendy640, KateRasheed
Signature 2
Source: Table S3
Description: Differential OTUs between mice with Inflammation and cancer
Abundance in Group 1: decreased abundance in Mice with dysplasia/cancer
Revision editor(s): Wendy640, KateRasheed
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 1 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after treatment of different AOM/DSS cycles
Abundance in Group 1: increased abundance in AOM/DSS Cycle 1 group
Revision editor(s): Wendy640, KateRasheed
Signature 3
Source: Table S4
Description: Differential OTUs after treatment of different AOM/DSS cycles
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 1 group
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Prevotella | ||
| Mediterraneibacter gnavus |
Revision editor(s): Wendy640, KateRasheed
Experiment 4
Subjects
- 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
- AOM/DSS Cycle 2 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 2 group
Revision editor(s): Wendy640, KateRasheed
Signature 2
Source: Table S4
Description: Differential OTUs after 2 cycles of AOM/DSS treatment, showing intermediate changes in the gut microbiota.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 2 group
Revision editor(s): Wendy640, KateRasheed
Experiment 5
Subjects
- 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
- AOM/DSS Cycle 3 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 3
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 3 group
Revision editor(s): Wendy640, KateRasheed
Signature 2
Source: Table S4
Description: Differential OTUs after 3 cycles of AOM/DSS treatment, indicating microbial changes at advanced disease stages.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 3 group
Revision editor(s): Wendy640, KateRasheed
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AOM/DSS Cycle 4 group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice treated with AOM/DSS cycle 4
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S4
Description: Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.
Abundance in Group 1: increased abundance in AOM/DSS Cycle 4 group
Revision editor(s): Wendy640, KateRasheed
Signature 2
Source: Table S4
Description: Differential OTUs after 4 cycles of AOM/DSS treatment, representing microbiota alterations during late-stage colorectal cancer.
Abundance in Group 1: decreased abundance in AOM/DSS Cycle 4 group
Revision editor(s): Wendy640, KateRasheed
