Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study
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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 Uniform resource identifier for web resources.
Authors
Cao Y, Shang F, Jin M, Deng S, Gu J, Mao F, Qin L, Wang J, Xue Y, Jiang Z, Cheng D, Liu L, Nie X, Liu T, Liu H, Cai K
Journal
BJS open
Year
2023
BACKGROUND: The relationship between intestinal obstruction due to colorectal cancer (CRC) and the gut microbiota remains largely unknown. The aim of this study was to investigate the potential association between alterations in gut microbiota and CRC in the presence of intestinal obstruction. METHODS: Patients with CRC with or without obstruction were recruited and compared using 1:1 propensity score matching (PSM). Total DNA from tumours and adjacent normal tissues of 84 patients and 36 frozen tumour tissues was extracted and amplified. 16S RNA sequencing was used to uncover differences in microbiota composition between the two groups. RESULTS: A total of 313 patients with CRC were recruited. Survival analysis demonstrated that patients in the obstruction group had shorter overall survival time and disease-free survival (DFS) time than those in the non-obstruction group. Microbial richness and diversity in tumour tissues of patients with obstruction were significantly higher than those of patients with no obstruction. The alpha diversity indices and beta diversity exhibited were different between the two groups (P < 0.05). At the phylum and genus levels, Bacteroidetes were significantly enriched in the tumour tissues of patients with obstruction. Alpha diversity in tumour tissues was closely related to specific microbiota. These findings were replicated in the 16S rRNA analyses from frozen samples. There were more Bacteroidetes in CRC patients with obstruction. CONCLUSIONS: Patients with obstructed CRC have worse prognosis and have differences in their microbiota. Higher levels of Bacteroides were observed in patients with obstructed CRC.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- 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
- patients with no obstruction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with obstruction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with obstructed colorectal cancer (CRC), presenting with intestinal obstruction symptoms at the time of admission.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 271
- 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)
- 1 week
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
- Kruskall-Wallis
- 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
- chemotherapy, sex, Matched on: "age at diagnosis" 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.age at diagnosis, Matched on: "bmi" 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.bmi, Matched on: "TNM stage" 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.TNM stage, Matched on: "histological grade" 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.histological grade, Matched on: "tumour size" 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.tumour size, Matched on: "tumour site" 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.tumour site
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Fig. 5e & 5f
Description: Phylum and genus level differences of microbial taxa between colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: increased abundance in patients with obstruction
Signature 2
Source: Fig. 5e & 5f
Description: Phylum and genus level differences of microbial taxa between colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: decreased abundance in patients with obstruction
| NCBI | Quality Control | Links |
|---|---|---|
| Armatimonadota | ||
| Clostridium | ||
| Cupriavidus | ||
| Cyanobacteriota | ||
| Deferribacteres | ||
| Fusobacteriota | ||
| Helicobacter | ||
| Leptotrichia | ||
| Pseudomonadota | ||
| Sphingomonas |
Experiment 2
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.45
- Matched on Factors on which subjects have been matched on in a case-control study
- chemotherapy, sex, Matched on: "bmi" 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.bmi, Matched on: "age at diagnosis" 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.age at diagnosis, Matched on: "TNM stage" 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.TNM stage, Matched on: "histological grade" 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.histological grade, Matched on: "tumour size" 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.tumour size, Matched on: "tumour site" 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.tumour site
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 5g
Description: Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: increased abundance in patients with obstruction
Revision editor(s): Ese
Signature 2
Source: Figure 5g
Description: Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: decreased abundance in patients with obstruction
Revision editor(s): Ese
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- frozen tumour tissues from patients with no obstruction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- frozen tumour tissues from patients with obstruction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tumour tissues from patients with newly diagnosed obstructed colorectal cancer (CRC), presenting with intestinal obstruction symptoms at the time of admission.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- chemotherapy, sex, Matched on: "age at diagnosis" 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.age at diagnosis, Matched on: "bmi" 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.bmi, Matched on: "TNM stage" 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.TNM stage, Matched on: "histological grade" 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.histological grade, Matched on: "tumour size" 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.tumour size, Matched on: "tumour site" 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.tumour site
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 6e & 6f
Description: Phylum and genus level differences of microbial taxa of frozen tumour tissues from colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: increased abundance in frozen tumour tissues from patients with obstruction
Revision editor(s): Ese
Signature 2
Source: Figure 6e & 6f
Description: Phylum and genus level differences of microbial taxa between patients with non-obstructed colorectal cancer and patients with obstructed colorectal cancer
Abundance in Group 1: decreased abundance in frozen tumour tissues from patients with obstruction
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Cupriavidus | ||
| Fusobacteriota | ||
| Helicobacter | ||
| Leptotrichia | ||
| Shigella | ||
| Sphingomonas | ||
| Pseudomonadota |
Revision editor(s): Ese
Experiment 4
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 7c
Description: Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between frozen tumour tissues from colorectal cancer (CRC) patients with no obstruction and colorectal cancer (CRC) patients with obstruction
Abundance in Group 1: increased abundance in frozen tumour tissues from patients with obstruction
Revision editor(s): Ese
Signature 2
Source: Figure 7c
Description: Linear discriminant analysis effect size (LEfSe) analysis showing significant differences in species diversity between patients with non-obstructed colorectal cancer and patients with obstructed colorectal cancer
Abundance in Group 1: decreased abundance in frozen tumour tissues from patients with obstruction
| NCBI | Quality Control | Links |
|---|---|---|
| Aquabacterium | ||
| Pseudomonadota |
Revision editor(s): Ese
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