Metagenomic analyses of the gut microbiota associated with colorectal adenoma
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N, Ohkusa T
Journal
PloS one
Year
2019
Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region of the 16S ribosomal RNA gene was performed. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to examine microbial dysbiosis, revealing significant differences in bacterial abundances between the healthy controls and CRA or intramucosal CRC patients. In particular, F. varium was statistically more abundant in patients with CRA and intramucosal CRC than in healthy subjects. Here, we present the metagenomic profile of CRA and intramucosal CRC and demonstrate that F. varium is at least partially involved in the pathogenesis of CRA and intramucosal CRC.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
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
- Intestine Bowel,Intestinal tract,Intestine,intestine
- 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
- 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 4B, Figure 7
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects.
Abundance in Group 1: decreased abundance in Intramucosal CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Sphingobium | ||
| Fusobacterium periodonticum | ||
| Fusobacterium perfoetens |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 4B, Figure 7
Description: Characterization of microbiomes in intramucosal CRC patients and healthy subjects.
Abundance in Group 1: increased abundance in Intramucosal CRC
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Fusobacterium | ||
| Parvimonas | ||
| Peptostreptococcus | ||
| Actinomyces | ||
| Fusobacteriia | ||
| Fusobacteriales | ||
| Fusobacteriaceae | ||
| Fusobacterium varium |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CRA (colorectal adenoma)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
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 | Quality Control | Links |
|---|---|---|
| Butyricimonas | ||
| Collinsella | ||
| Mitsuokella | ||
| Deltaproteobacteria | ||
| Desulfovibrionales | ||
| Synergistaceae | ||
| Comamonas | ||
| Desulfovibrionaceae |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 8B, Figure 9
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 | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Erysipelotrichaceae | ||
| Veillonella |
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Differences from previous experiment shown
Subjects
- 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,Colorectal 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 2B, Figure 6
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: increased abundance in CRA (colorectal adenoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnobacterium | ||
| Butyricimonas | ||
| Salmonella | ||
| Comamonas | ||
| Moraxellaceae | ||
| Fusobacterium varium |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 2B, Figure 6
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: decreased abundance in CRA (colorectal adenoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium | ||
| Parvimonas | ||
| Fusobacterium | ||
| Fusobacterium periodonticum | ||
| Fusobacterium nucleatum | ||
| Fusobacteriia | ||
| Fusobacteriales | ||
| Fusobacteriaceae |
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