Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model
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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
- United States of America
- 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
- Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- 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
- T-Test
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2B, 2E and S7
Description: Relative abundances of microbial taxa at phylum level.
Abundance in Group 1: increased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota | ||
| Verrucomicrobiota | ||
| Alistipes inops | ||
| Romboutsia ilealis |
Revision editor(s): Joiejoie, PreciousChijioke
Signature 2
Source: Fig. 2B, 2E and S7
Description: Relative abundances of microbial taxa at phylum level.
Abundance in Group 1: decreased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Bifidobacterium pseudolongum |
Revision editor(s): PreciousChijioke, Victoria
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2D
Description: Differential bacterial species.
Abundance in Group 1: increased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis | ||
| Alistipes inops |
Revision editor(s): PreciousChijioke, Victoria
Signature 2
Source: Fig. 2D
Description: Differential bacterial species.
Abundance in Group 1: decreased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudolongum |
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 50 ppm iron
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed an iron excess (500 ppm) diet.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2C
Description: Relative abundances of microbial taxa at family level.
Abundance in Group 1: increased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Joiejoie, PreciousChijioke
Signature 2
Source: Fig. 2C
Description: Relative abundances of microbial taxa at family level.
Abundance in Group 1: decreased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Muribaculaceae |
Revision editor(s): PreciousChijioke, Victoria
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2B, 2E and S7
Description: Relative abundances of microbial taxa at phylum level.
Abundance in Group 1: increased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota | ||
| Romboutsia ilealis | ||
| Verrucomicrobiota |
Revision editor(s): PreciousChijioke, Victoria
Signature 2
Source: Fig. 2B, 2E and S7
Description: Relative abundances of microbial taxa at phylum level.
Abundance in Group 1: decreased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Faecalibaculum rodentium | ||
| Bifidobacterium pseudolongum |
Revision editor(s): PreciousChijioke
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2D
Description: Differential bacterial species.
Abundance in Group 1: increased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 2D
Description: Differential bacterial species.
Abundance in Group 1: decreased abundance in FMT-CRC (Fecal microbiota transplantation from Colorectal cancer patients) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudolongum | ||
| Faecalibaculum rodentium |
Revision editor(s): PreciousChijioke
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 50 ppm iron
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from healthy human controls and were fed an iron excess (500 ppm) diet.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Fig. 2C
Description: Relative abundances of microbial taxa at family level.
Abundance in Group 1: increased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig. 2C
Description: Relative abundances of microbial taxa at family level.
Abundance in Group 1: decreased abundance in FMT-HC (Fecal microbiota transplantation from healthy controls) mice fed 500 ppm iron
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Streptococcaceae |
Revision editor(s): PreciousChijioke, Victoria
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice fed with Saline 50ppm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed with Saline 500ppm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed a saline (500 ppm) diet.
- 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
- Statistical test
- ANOVA
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Fig. 4B
Description: Fecal levels of F. rodentium (Fr) and H. biformis (Hb) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: decreased abundance in Mice fed with Saline 500ppm
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibaculum rodentium |
Revision editor(s): PreciousChijioke, Victoria
Experiment 8
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with a Saline (500 ppm) diet.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5B
Description: Fecal levels of A. inops (Ai) and B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: increased abundance in Mice fed with Saline 500ppm
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes inops |
Revision editor(s): PreciousChijioke, Victoria
Signature 2
Source: Figure 5B
Description: Fecal levels of A. inops (Ai) and B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: decreased abundance in Mice fed with Saline 500ppm
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudolongum |
Revision editor(s): Victoria
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mice fed with Saline 500ppm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed with F. rodentium strain ALO17 (Fr) 500ppm by weekly gavage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with F. rodentium strain ALO17 (Fr) 500ppm by weekly gavage.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Fecal levels of F. rodentium (Fr) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: increased abundance in Mice fed with F. rodentium strain ALO17 (Fr) 500ppm by weekly gavage
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibaculum rodentium |
Revision editor(s): Victoria
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed with H. biformis strain VPI C17 - 5 (Hb) 500ppm by weekly gavage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with H. biformis strain VPI C17 - 5 (Hb) 500ppm by weekly gavage.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Fecal levels of H. biformis (Hb) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: increased abundance in Mice fed with H. biformis strain VPI C17 - 5 (Hb) 500ppm by weekly gavage
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemanella biformis |
Revision editor(s): Victoria
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed with Alistipes inops strain 627 (Ai) 500ppm by weekly gavage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with Alistipes inops strain 627 (Ai) 500ppm by weekly gavage.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5B
Description: Fecal levels of A. inops (Ai) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: increased abundance in Mice fed with Alistipes inops strain 627 (Ai) 500ppm by weekly gavage
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes inops |
Revision editor(s): Victoria
Experiment 12
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice fed with Bifidobacterium pseudolongum strain 28 T (Bp) 500ppm by weekly gavage
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to mice that received fecal microbiota transplantation from Colorectal cancer patients and were fed with Bifidobacterium pseudolongum strain 28 T (Bp) 500ppm by weekly gavage.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5B
Description: Fecal levels of B. pseudolongum (Bp) quantified by real-time PCR in mice at endpoint.
Abundance in Group 1: increased abundance in Mice fed with Bifidobacterium pseudolongum strain 28 T (Bp) 500ppm by weekly gavage
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudolongum |
Revision editor(s): Victoria
