Human intestinal lumen and mucosa-associated microbiota in patients with 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.
URI
Authors
Chen W, Liu F, Ling Z, Tong X, Xiang C
Journal
PloS one
Year
2012
Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; however the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
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
- 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 volunteers (swc)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients (swp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- 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
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Sanger
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: decreased abundance in CRC patients (swp)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Catenibacterium | ||
| Faecalibacterium | ||
| Blautia | ||
| Gardnerella | ||
| Bifidobacterium | ||
| Lachnospira |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: increased abundance in CRC patients (swp)
| NCBI | Quality Control | Links |
|---|---|---|
| Catonella | ||
| Fusobacterium | ||
| Gemella | ||
| Klebsiella | ||
| Mogibacterium | ||
| Peptostreptococcus | ||
| Porphyromonas | ||
| Selenomonas | ||
| Filifactor |
Revision editor(s): Jeshudy
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paracancerous tissue (pa10t)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous tissue (cat)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, colorectal cancer tissue Note: group 0 = paracancerous tissue 10-20 cm from cancerous tissue
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "patient" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.patient
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 3
Description: Phylotypes significantly different between cat and pa10t.
Abundance in Group 1: decreased abundance in cancerous tissue (cat)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Paraprevotella | ||
| Phascolarctobacterium | ||
| Parabacteroides | ||
| Faecalibacterium | ||
| Alphaproteobacteria | ||
| Methylobacterium | ||
| Acidocella |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 3
Description: Phylotypes significantly different between cat and pa10t.
Abundance in Group 1: increased abundance in cancerous tissue (cat)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli |
Revision editor(s): Jeshudy
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paracancerous tissue (pa2t)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, cancerous tissue. Note: Group 0 = paracancerous tissue 2-5 cm from cancerous tissue
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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Table 3
Description: Phylotypes significantly different between cat and pa2t
Abundance in Group 1: decreased abundance in cancerous tissue (cat)
| NCBI | Quality Control | Links |
|---|---|---|
| Ochrobactrum | ||
| Alphaproteobacteria |
Revision editor(s): Jeshudy
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy volunteers (stc)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients (stp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, diagnosed with colorectal cancer (stp = stool sample)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-18
Source: Figure 4B
Description: Figure 4. Relative abundance of significantly different genera between CRC patients and healthy controls. Genera differing between stp and stc.
Abundance in Group 1: increased abundance in CRC patients (stp)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus | ||
| Anaerotruncus | ||
| Collinsella | ||
| Eubacterium | ||
| Mogibacterium | ||
| Slackia | ||
| Paraprevotella | ||
| Desulfovibrio | ||
| Porphyromonas | ||
| Peptostreptococcus |
Revision editor(s): Jeshudy
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