Potential of fecal microbiota for early-stage detection of colorectal cancer
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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.
Authors
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
Journal
Molecular systems biology
Year
2014
Keywords:
cancer screening, colorectal cancer, fecal biomarkers, human gut microbiome, metagenomics
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Curated date: 2022/01/10
Curator: Itslanapark
Revision editor(s): WikiWorks, Fatima, Itslanapark, Peace Sandy
Subjects
- Location of subjects
- France
- 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 carcinoma cancer of large bowel,cancer of large intestine,cancer of the large bowel,cancer of the large intestine,carcinoma of colorectum,carcinoma of large bowel,carcinoma of large intestine,carcinoma of the large bowel,carcinoma of the large intestine,colorectal (colon or rectal) cancer,colorectal cancer,colorectal carcinoma,colorectum carcinoma,CRC,large bowel cancer,large bowel carcinoma,large intestine cancer,large intestine carcinoma,Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoplasia-free
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients referred for colonoscopy that had cancerous tumors
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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)
- .1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
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 2023-3-7
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa
Abundance in Group 1: increased abundance in CRC patients
Revision editor(s): Itslanapark, Fatima
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa
Abundance in Group 1: decreased abundance in CRC patients
Revision editor(s): Itslanapark, Fatima
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma cancer of large bowel,cancer of large intestine,cancer of the large bowel,cancer of the large intestine,carcinoma of colorectum,carcinoma of large bowel,carcinoma of large intestine,carcinoma of the large bowel,carcinoma of the large intestine,colorectal (colon or rectal) cancer,colorectal cancer,colorectal carcinoma,colorectum carcinoma,CRC,large bowel cancer,large bowel carcinoma,large intestine cancer,large intestine carcinoma,Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adenoma patients
- 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between CRC and Adenoma patients
Abundance in Group 1: increased abundance in CRC patients
Revision editor(s): Fatima
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between CRC and Adenoma patients
Abundance in Group 1: decreased abundance in CRC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter rectalis | ||
| Eubacterium |
Revision editor(s): Fatima
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoplasia free
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adenoma patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S2
Description: significant differences in the abundance of specific taxa between Adenoma patients and neoplasia free
Abundance in Group 1: decreased abundance in Adenoma patients
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus |
Revision editor(s): Fatima
Experiment 4
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neoplasia free control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC
- Group 0 sample size Number of subjects in the control (unexposed) group
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S3
Description: Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas)
Abundance in Group 1: increased abundance in CRC
Revision editor(s): Fatima
Signature 2
Reviewed Marked as Reviewed by Fatima on 2023-3-7
Source: Supplementary Figure S3
Description: Microbial taxa significantly different between CRC patients to the control group (consisting of neoplasia-free and ones with small adenomas)
Abundance in Group 1: decreased abundance in CRC
Revision editor(s): Fatima
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