Metagenomic analyses of the gut microbiota associated with colorectal adenoma
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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 (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Intestine Bowel,Intestinal tract,Intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- intramucosal CRCintramucosal CRC
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intramucosal CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum
- 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
- 24
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
Signature 1
Source: Figure 4B
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.
Abundance in Group 1: decreased abundance in Intramucosal CRC
NCBI | Links |
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Megamonas | |
Sphingobium ⚠ |
Revision editor(s): Jeshudy
Signature 2
Source: Figure 4B
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.
Abundance in Group 1: increased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Actinobacillus | |
Fusobacterium | |
Parvimonas | |
Peptostreptococcus | |
Actinomyces |
Revision editor(s): Jeshudy
Signature 3
Source: Figure 7
Description: Characterization of Fusobacterium spp. in intramucosal CRC patients and healthy subjects. (A) Histogram of the LDA scores (log10) computed for Fusobacterium spp. Features that were differentially abundant in intramucosal CRC and healthy subjects. (B) Relative abundances of the groups of Fusobacterium spp. displaying significant differences between intramucosal CRC and healthy subjects.
Abundance in Group 1: decreased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Fusobacterium periodonticum | |
Fusobacterium perfoetens |
Revision editor(s): Jeshudy
Signature 4
Source: Figure 7
Description: Characterization of Fusobacterium spp. in intramucosal CRC patients and healthy subjects. (A) Histogram of the LDA scores (log10) computed for Fusobacterium spp. Features that were differentially abundant in intramucosal CRC and healthy subjects. (B) Relative abundances of the groups of Fusobacterium spp. displaying significant differences between intramucosal CRC and healthy subjects.
Abundance in Group 1: increased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Fusobacterium varium |
Revision editor(s): Jeshudy
Experiment 2
Subjects
- Location of subjects
- Japan
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Intestine Bowel,Intestinal tract,Intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- intramucosal CRCintramucosal CRC
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CRA (colorectal adenoma)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intramucosal CRC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Intramucosal CRC is in its earliest stage (stage 0) and is also known as carcinoma in situ or intramucosal carcinoma. Intramucosal CRC has not yet grown beyond the inner mucosal layer of the colorectum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- 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
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
Signature 1
Source: Figure 8B
Description: Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.
Abundance in Group 1: increased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Butyricimonas | |
Collinsella | |
Mitsuokella | |
Deltaproteobacteria | |
Desulfovibrionales | |
Synergistaceae | |
Comamonas ⚠ | |
Desulfovibrionaceae |
Revision editor(s): Jeshudy
Signature 2
Source: Figure 8B
Description: Characterization of microbiomes in patients with CRA and intramucosal CRC by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features that were differentially abundant in patients with CRA and intramucosal CRC.
Abundance in Group 1: decreased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Megamonas | |
Erysipelotrichaceae |
Revision editor(s): Jeshudy
Signature 3
Source: Figure 9
Description: Histogram of the gut microbiota relative abundances in patients with CRA and intramucosal CRC. Relative abundances of the groups of bacteria that displayed significant differences between CRA patients and healthy subjects
Abundance in Group 1: increased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Collinsella | |
Deltaproteobacteria | |
Desulfovibrionales | |
Synergistaceae | |
Erysipelotrichaceae |
Revision editor(s): Jeshudy
Signature 4
Source: Figure 9
Description: Histogram of the gut microbiota relative abundances in patients with CRA and intramucosal CRC. Relative abundances of the groups of bacteria that displayed significant differences between CRA patients and healthy subjects
Abundance in Group 1: decreased abundance in Intramucosal CRC
NCBI | Links |
---|---|
Veillonella |
Revision editor(s): Jeshudy
Experiment 3
Subjects
- Location of subjects
- Japan
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Intestine Bowel,Intestinal tract,Intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRA (colorectal adenoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal adenoma, as diagnosed after a complete colonoscopic exampination
- 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
- 47
- 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
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- increased
Signature 1
Source: Figure 2B
Description: Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. (A) Taxonomic representation of statistically and biologically consistent differences in CRA and healthy subjects. (B) Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.
Abundance in Group 1: decreased abundance in CRA (colorectal adenoma)
NCBI | Links |
---|---|
Lachnobacterium | |
Butyricimonas | |
Salmonella ⚠ | |
Comamonas ⚠ | |
Moraxellaceae |
Revision editor(s): Jeshudy
Signature 2
Source: Figure 2B
Description: Characterization of microbiomes in CRA patients and healthy subjects by LEfSe analysis and LDA. Histogram of the LDA scores (log10) computed for features with differential abundance in CRA patients and healthy subjects.
Abundance in Group 1: increased abundance in CRA (colorectal adenoma)
NCBI | Links |
---|---|
Atopobium | |
Parvimonas | |
Fusobacterium |
Revision editor(s): Jeshudy
Signature 3
Source: Figure 6
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.
Abundance in Group 1: decreased abundance in CRA (colorectal adenoma)
NCBI | Links |
---|---|
Fusobacterium periodonticum | |
Fusobacterium nucleatum |
Revision editor(s): Jeshudy
Signature 4
Source: Figure 6
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects. Histogram of the LDA scores (log10) computed for features differentially abundant in CRC patients and healthy subjects.
Abundance in Group 1: increased abundance in CRA (colorectal adenoma)
NCBI | Links |
---|---|
Fusobacterium varium |
Revision editor(s): Jeshudy