Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in 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
- Japan
- 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
- 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
- healthy control (normal and a few polyps)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- stage I/II (SI/II)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage I and II CRCs
- Group 0 sample size Number of subjects in the control (unexposed) group
- 251
- Group 1 sample size Number of subjects in the case (exposed) group
- 111
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None specified
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.005
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in stage I/II (SI/II)
Revision editor(s): Jeshudy
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in stage I/II (SI/II)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira eligens | ||
| Lachnospira multipara |
Revision editor(s): Jeshudy
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- stage III/IV (SIII/IV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage III and IV CRCs
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Phylum distribution of the number of species that are either elevated or depleted in each of the four stages compared to the healthy controls.
Abundance in Group 1: increased abundance in stage III/IV (SIII/IV)
Revision editor(s): Jeshudy
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in stage III/IV (SIII/IV)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira eligens | ||
| Lachnospira multipara |
Revision editor(s): Jeshudy
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- S0
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- stage 0/pTis CRC (S0)
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in S0
Revision editor(s): Jeshudy
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in S0
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira multipara | ||
| Lachnospira eligens |
Revision editor(s): Jeshudy
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- multiple polypoid adenomas with low- grade dysplasia (MP, more than three adenomas, mostly more than five adenomas)
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: increased abundance in MP
| NCBI | Quality Control | Links |
|---|---|---|
| Lancefieldella parvula | ||
| Fusobacterium nucleatum | ||
| Schaalia odontolytica | ||
| Phascolarctobacterium succinatutens | ||
| Selenomonas sputigena | ||
| Oleidesulfovibrio vietnamensis |
Revision editor(s): Jeshudy
Signature 2
Source: Figure 2B
Description: Species abundances were assessed for significant elevation or depletion (P< 0.005; one-sided Mann–Whitney U test) in each of the four stages, MP (n= 67), S0 (n= 73), SI/II (n= 111) and SIII/IV (n= 74), compared to the healthy controls (n= 251).
Abundance in Group 1: decreased abundance in MP
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium longum subsp. longum | ||
| Lachnospira multipara | ||
| Lachnospira eligens |
Revision editor(s): Jeshudy
