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
Gao Z, Guo B, Gao R, Zhu Q, Qin H
Journal
Frontiers in microbiology
Year
2015
Keywords:
colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon
The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals differed significantly. Firmicutes and Fusobacteria were over-represented whereas Proteobacteria was under-represented in CRC patients. In addition, Lactococcus and Fusobacterium exhibited a relatively higher abundance while Pseudomonas and Escherichia-Shigella was reduced in cancerous tissues compared to adjacent non-cancerous tissues. Meanwhile, the overall microbial structures of proximal and distal colon cancerous tissues were similar; but certain potential pro-oncogenic pathogens were different. These results suggested that the mucosa-associated microbiota is dynamically associated with CRC, which may provide evidences for microbiota-associated diagnostic, prognostic, preventive, and therapeutic strategies for CRC.
Experiment 1
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Subjects
- Location of subjects
- China
- 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
- Colorectal mucosa Colorectal mucosa,colorectal mucosa
- 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 controls
- 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
- Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Fisher's Exact Test
- Chi-Square
- T-Test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: Figure 2B, Figure 3
Description: Different structures of gut microbiota between healthy individuals and CRC patients
Abundance in Group 1: increased abundance in Colorectal Cancer Patients
Revision editor(s): Andre, Deacme, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: Figure 2, Figure 3
Description: Different structures of gut microbiota between healthy individuals and CRC patients
Abundance in Group 1: decreased abundance in Colorectal Cancer Patients
Revision editor(s): Andre, Deacme, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- adjacent non-cancerous tissues
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous tissues
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
- Statistical test
- Fisher's Exact Test
- Chi-Square
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: Figure 2D
Description: The dominant genera of group cancerous compared to non-cancerous mucosa
Abundance in Group 1: increased abundance in cancerous tissues
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lactococcus | ||
| Fusobacterium | ||
| Prevotella | ||
| Streptococcus |
Experiment 3
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sigmoid neoplasm neoplasm of sigmoid colon,sigmoid colon neoplasm,sigmoid colon neoplasm (disease),sigmoid colon tumor,sigmoid neoplasm,tumor of sigmoid colon,Sigmoid neoplasm
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Proximal Colon Cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Distal Colorectal Cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: FIGURE 4
Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)
Abundance in Group 1: increased abundance in Distal Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Fusobacterium | ||
| Leptotrichia |
Revision editor(s): Andre, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
Source: FIGURE 4
Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)
Abundance in Group 1: decreased abundance in Distal Colorectal Cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcus | ||
| Prevotella | ||
| Pyramidobacter sp. | ||
| Selenomonas |
Revision editor(s): Andre, ChiomaBlessing
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