Gut microbiome development along the colorectal adenoma-carcinoma sequence
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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
Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, Huber-Schönauer U, Niederseer D, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Arumugam M, Tilg H, Datz C, Wang J
Journal
Nature communications
Year
2015
Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gut microbe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions enriched in each group. An analysis of potential risk factors indicates that high intake of red meat relative to fruits and vegetables appears to associate with outgrowth of bacteria that might contribute to a more hostile gut environment. These findings suggest that faecal microbiome-based strategies may be useful for early diagnosis and treatment of colorectal adenoma or carcinoma.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Subjects
- Location of subjects
- Austria
- 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 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 Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Advanced Colorectal Adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- colorectal adenoma patients The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine, Oberndorf Hospital.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4a
Description: Control versus advanced adenoma (n = 55 and 42).
Abundance in Group 1: increased abundance in Advanced Colorectal Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Paraprevotella clara | ||
| Phocaeicola dorei | ||
| Phocaeicola massiliensis |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4a
Description: Control versus advanced adenoma (n = 55 and 42).
Abundance in Group 1: decreased abundance in Advanced Colorectal Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis | ||
| Streptococcus mutans |
Revision editor(s): Jeshudy
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- colorectal cancer patients The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine, Oberndorf Hospital.
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4c
Description: Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.
Abundance in Group 1: decreased abundance in Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces viscosus | ||
| Clostridium sp. | ||
| Streptococcus mutans | ||
| Streptococcus thermophilus | ||
| Bifidobacterium animalis |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4c
Description: Control versus carcinoma (n = 55 and 41). For all MLGs containing >100 genes, the direction of enrichment was determined by Wilcoxon rank-sum test (P < 0.05, Supplementary Data 3). Size of the nodes scales with the number of genes (102~3613) in the MLG.
Abundance in Group 1: increased abundance in Colorectal Cancer
Revision editor(s): Jeshudy
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Advanced Colorectal Adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- colorectal adenoma patients The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine, Oberndorf Hospital.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4b
Description: Advanced adenoma vs carcinoma (n = 42, 41).
Abundance in Group 1: decreased abundance in Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. | ||
| Streptococcus thermophilus | ||
| Bifidobacterium animalis | ||
| Actinomyces viscosus |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4b
Description: Advanced adenoma vs carcinoma (n = 42, 41).
Abundance in Group 1: increased abundance in Colorectal Cancer
Revision editor(s): Jeshudy
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