Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers
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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
Fang CY, Chen JS, Hsu BM, Hussain B, Rathod J, Lee KH
Journal
Microorganisms
Year
2021
Keywords:
biomarker, colorectal cancer, functional predictions, gut microbial dysbiosis, gut microbiota, metagenomics, prognosis
Despite advances in the characterization of colorectal cancer (CRC), it still faces a poor prognosis. There is growing evidence that gut microbiota and their metabolites potentially contribute to the development of CRC. Thus, microbial dysbiosis and their metabolites associated with CRC, based on stool samples, may be used to advantage to provide an excellent opportunity to find possible biomarkers for the screening, early detection, prevention, and treatment of CRC. Using 16S rRNA amplicon sequencing coupled with statistical analysis, this study analyzed the cause-effect shift of the microbial taxa and their metabolites that was associated with the fecal gut microbiota of 17 healthy controls, 21 polyps patients, and 21 cancer patients. The microbial taxonomic shift analysis revealed striking differences among the healthy control, polyps and cancer groups. At the phylum level, Synergistetes was reduced significantly in the polyps group compared to the healthy control and cancer group. Additionally, at the genus level and in association with the cancer group, a total of 12 genera were highly enriched in abundance. In contrast, only Oscillosprira was significantly higher in abundance in the healthy control group. Comparisons of the polyps and cancer groups showed a total of 18 significantly enriched genera. Among them, 78% of the genera associated with the cancer group were in higher abundance, whereas the remaining genera showed a higher abundance in the polyps group. Additionally, the comparison of healthy control and polyp groups showed six significantly abundant genera. More than 66% of these genera showed a reduced abundance in the polyps group than in healthy controls, whereas the remaining genera were highly abundant in the polyps group. Based on tumor presence and absence, the abundance of Olsenella and Lactobacillus at the genus level was significantly reduced in the patient group compared to healthy controls. The significant microbial function prediction revealed an increase in the abundance of metabolites in the polyps and cancer groups compared to healthy controls. A correlation analysis revealed a higher contribution of Dorea in the predicted functions. This study showed dysbiosis of gut microbiota at the taxonomic level and their metabolic functions among healthy subjects and in two stages of colorectal cancer, including adenoma and adenocarcinoma, which might serve as potential biomarkers for the early diagnosis and treatment of CRC.
Experiment 1
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Subjects
- Location of subjects
- Taiwan
- 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 subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persons aged 25–95 years old with cancerous large intestine tumor symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- Metastats
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: differential abundance of bacteria in patients with colorectal cancer and healthy controls
Abundance in Group 1: increased abundance in colorectal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Acinetobacter | ||
| Coriobacterium | ||
| Coxiella | ||
| Leuconostoc | ||
| Limnobacter | ||
| Methanobrevibacter | ||
| Rothia | ||
| Sporobacterium | ||
| Succinatimonas | ||
| Haloferula |
Revision editor(s): Itslanapark, Chloe
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: differential abundance of bacteria in patients with colorectal cancer and healthy controls
Abundance in Group 1: decreased abundance in colorectal cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira |
Revision editor(s): Itslanapark, Chloe
Experiment 2
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Intestinal polyp intestinal polyp,intestinal polyp (disease),Intestinal Polyps,Polyp, Intestinal,Polyps, Intestinal,Intestinal polyp
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- polyps patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persons aged 25–95 years old with polyps
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.
Abundance in Group 1: increased abundance in polyps patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Mitsuokella |
Revision editor(s): Chloe
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.
Abundance in Group 1: decreased abundance in polyps patients
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Enterococcus | ||
| Pseudomonas | ||
| Cytophaga |
Revision editor(s): Chloe
Experiment 3
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- polyps patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persons aged 25–95 years old with cancerous large intestine tumor symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.
Abundance in Group 1: increased abundance in cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Campylobacter | ||
| Enterococcus | ||
| Slackia | ||
| Pyramidobacter | ||
| Coriobacterium | ||
| Methanobrevibacter | ||
| Peptostreptococcus | ||
| Abiotrophia | ||
| Coxiella | ||
| Haloferula | ||
| Leuconostoc | ||
| Weissella |
Revision editor(s): Chloe
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description:
Abundance in Group 1: decreased abundance in cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonas | ||
| Sporobacterium | ||
| Oscillospira | ||
| Mitsuokella | ||
| Streptobacillus |
Revision editor(s): Chloe
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