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
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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 | Links |
|---|---|
| Bacteroides | |
| Ruminiclostridium | |
| unclassified Erysipelotrichaceae |
Revision editor(s): Mary Bearkland
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 | Links |
|---|---|
| Desulfovibrio | |
| Lachnospiraceae | |
| Muribaculaceae |
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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.
- 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
Signature 1
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
Revision editor(s): Mary Bearkland
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 | Links |
|---|---|
| Desulfovibrio | |
| Muribaculaceae | |
| Lachnospiraceae |
Revision editor(s): Mary Bearkland
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Coli
- 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.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Signature 1
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
Revision editor(s): Mary Bearkland
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 | Links |
|---|---|
| Bacteroides | |
| Erysipelotrichaceae | |
| Ruminiclostridium |
Revision editor(s): Mary Bearkland
Experiment 4
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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 | Links |
|---|---|
| Bacteroidaceae bacterium | |
| Bacteroides ovatus | |
| Bacteroides xylanisolvens | |
| Parabacteroides sp. | |
| unclassified Bacteroidales | |
| uncultured prokaryote |
Revision editor(s): Mary Bearkland
Signature 2
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
Experiment 5
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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.
- 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
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 | 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
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- coli
- 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.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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 | 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
