Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway
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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
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Fatima, Peace Sandy
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Coli
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group). Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
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).
- relative abundances
- Statistical test
- ANOVA
- 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: supp fig 1B
Description: Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: increased abundance in Coli
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Ruminiclostridium | ||
| Parabacteroides | ||
| Erysipelotrichaceae |
Revision editor(s): Mary Bearkland, Atrayees
Signature 2
Source: supp fig 1B
Description: Supplementary Figure 1.Compositional differences in the gut microbiome are associated with responses to PD-1 antibody immunotherapy (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: decreased abundance in Coli
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrio | ||
| Lachnospiraceae | ||
| Bacteroidales | ||
| Parasutterella | ||
| Eubacteriales |
Revision editor(s): Mary Bearkland, Atrayees
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vanc
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group). Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V4
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Curated date: 2022/09/17
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Merit, Atrayees
Source: supp fig 1B
Description: Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: increased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Escherichia/Shigella sp. | ||
| Lactobacillus | ||
| Parabacteroides | ||
| Parasutterella | ||
| Prevotellaceae | ||
| Roseburia | ||
| unclassified Enterobacteriaceae | ||
| Lactobacillales | ||
| Eubacteriales |
Revision editor(s): Mary Bearkland, Merit, Atrayees
Signature 2
Source: supp fig 1B
Description: Supplementary Figure 1(B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: decreased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrio | ||
| Lachnospiraceae | ||
| Bacteroidales | ||
| Erysipelotrichaceae |
Revision editor(s): Mary Bearkland, Atrayees
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Coli
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Curated date: 2022/09/18
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Merit, Atrayees
Source: supp fig 1B
Description: Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: increased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Escherichia/Shigella sp. | ||
| Lactobacillus | ||
| Parabacteroides | ||
| Parasutterella | ||
| Prevotellaceae | ||
| Roseburia | ||
| unclassified Enterobacteriaceae | ||
| Ruminiclostridium |
Revision editor(s): Mary Bearkland, Merit, Atrayees
Signature 2
Source: supp fig 1B
Description: Supplementary Figure 1 (B) Bar plot of compositional differences at genus level in the gut microbiome of three groups of mice by one-way ANOVA.
Abundance in Group 1: decreased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Erysipelotrichaceae | ||
| Ruminiclostridium | ||
| Desulfovibrio | ||
| Bacteroidales | ||
| Lachnospiraceae |
Revision editor(s): Mary Bearkland, Atrayees
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Coli
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 mice were treated with colistin (2 mg/ml) in sterile drinking water (Coli group). Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Signature 1
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Control vs. Coli
Abundance in Group 1: increased abundance in Coli
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae bacterium | ||
| Bacteroides ovatus | ||
| Bacteroides xylanisolvens | ||
| Parabacteroides sp. | ||
| unclassified Bacteroidales | ||
| uncultured prokaryote |
Revision editor(s): Mary Bearkland
Signature 2
Curated date: 2022/09/18
Curator: Mary Bearkland
Revision editor(s): Mary Bearkland, Merit, Atrayees
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Control vs. Coli
Abundance in Group 1: decreased abundance in Coli
Revision editor(s): Mary Bearkland, Merit, Atrayees
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vanc
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 mice were treated with vancomycin alone (0.25 mg/ml) in sterile drinking water (Vanc group) Mice (in all groups) were then subcutaneously injected into the right axillary with 0.25 live CT26 tumor cells.
Lab analysis
Statistical Analysis
Signature 1
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Control vs. Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.
Abundance in Group 1: increased abundance in Vanc
Revision editor(s): Mary Bearkland
Signature 2
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Control vs. Vanc group of mice before PD-1 antibody treatment by one-way ANOVA.
Abundance in Group 1: decreased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. CAG:927 | ||
| Firmicutes bacterium ASF500 | ||
| Lachnospiraceae bacterium A4 | ||
| Phocaeicola massiliensis | ||
| Prevotella sp. CAG:1031 | ||
| Prevotella sp. CAG:873 |
Revision editor(s): Mary Bearkland
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- coli
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
Signature 1
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.
Abundance in Group 1: increased abundance in Vanc
Revision editor(s): Mary Bearkland
Signature 2
Source: supp fig 2
Description: Bar plot of compositional differences at species level in the Vanc vs.Coli groups of mice before PD-1 antibody treatment by one-way ANOVA.
Abundance in Group 1: decreased abundance in Vanc
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides sp. CAG:927 | ||
| Prevotella sp. CAG:1031 | ||
| Prevotella sp. CAG:873 | ||
| Prevotella sp. CAG:279 | ||
| Phocaeicola vulgatus | ||
| Lachnospiraceae bacterium A4 | ||
| Firmicutes bacterium ASF500 |
Revision editor(s): Mary Bearkland
