The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma
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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
Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EE, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TG, de Boer NK
Journal
Gut microbes
Year
2022
Keywords:
Omics, adenoma, biomarker, colorectal cancer, surveillance
The risk of recurrent dysplastic colonic lesions is increased following polypectomy. Yield of endoscopic surveillance after adenoma removal is low, while interval colorectal cancers occur. To longitudinally assess the dynamics of fecal microbiota and amino acids in the presence of adenomatous lesions and after their endoscopic removal. In this longitudinal case-control study, patients collected fecal samples prior to bowel preparation before scheduled colonoscopy and 3 months after this intervention. Based on colonoscopy outcomes, patients with advanced adenomas and nonadvanced adenomas (0.5-1.0 cm) who underwent polypectomy during endoscopy (n = 19) were strictly matched on age, body-mass index, and smoking habits to controls without endoscopic abnormalities (n = 19). Microbial taxa were measured by 16S RNA sequencing, and amino acids (AA) were measured by high-performance liquid chromatography (HPLC). Adenoma patients were discriminated from controls based on AA and microbial composition. Levels of proline (p = .001), ornithine (p = .02) and serine (p = .02) were increased in adenoma patients compared to controls but decreased to resemble those of controls after adenoma removal. These AAs were combined as a potential adenoma-specific panel (AUC 0.79(0.64-0.94)). For bacterial taxa, differences between patients with adenomas and controls were found (Bifidobacterium spp.↓, Anaerostipes spp.↓, Butyricimonas spp.↑, Faecalitalea spp.↑ and Catenibacterium spp.↑), but no alterations in relative abundance were observed after polypectomy. Furthermore, Faecalitalea spp. and Butyricimonas spp. were significantly correlated with adenoma-specific amino acids. We selected an amino acid panel specifically increased in the presence of adenomas and a microbial signature present in adenoma patients, irrespective of polypectomy. Upon validation, these panels may improve the effectiveness of the surveillance program by detection of high-risk individuals and determination of surveillance endoscopy timing, leading to less unnecessary endoscopies and less interval cancer.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Subjects
- Location of subjects
- Netherlands
- 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 adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-adenoma group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenoma group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8]. PRIOR to polypectomy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- 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)
- 3 months prior to study inclusion and 3 months prior to second sample
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 2
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, smoking behavior
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2
Description: Distribution of selected taxa for adenomas versus controls at baseline
Abundance in Group 1: increased abundance in adenoma group
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricimonas | ||
| Catenibacterium | ||
| Sutterella |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2
Description: Distribution of selected taxa for adenomas versus controls at baseline
Abundance in Group 1: decreased abundance in adenoma group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Bifidobacterium | ||
| Faecalitalea | ||
| Candidatus Gastranaerophilales |
Revision editor(s): Jeshudy
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- 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
- smoking status, age, body mass index
Alpha Diversity
- Richness Number of species
- unchanged
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8]. POST polypectomy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2
Description: Distribution of selected taxa for adenomas versus controls at follow-up.
Abundance in Group 1: decreased abundance in adenoma group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Gastranaerophilales | ||
| Bifidobacterium |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2
Description: Distribution of selected taxa for adenomas versus controls at follow-up.
Abundance in Group 1: increased abundance in adenoma group
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterella |
Revision editor(s): Jeshudy
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- adenoma group pre-polypectomy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenoma group post-polypectomy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "subject" 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.subject
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 3
Description: Distribution of selected taxa for baseline versus follow-up.
Abundance in Group 1: increased abundance in adenoma group post-polypectomy
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| unclassified Candidatus Izimaplasma | ||
| unclassified Enterobacteriaceae | ||
| unclassified Puniceicoccaceae | ||
| unclassified Clostridium |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2
Description: Distribution of selected taxa for adenomas at baseline and follow-up.
Abundance in Group 1: increased abundance in adenoma group post-polypectomy
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Gastranaerophilales |
Revision editor(s): Jeshudy
Experiment 5
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group pre-endoscopy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- control group post-endoscopy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with a successful endoscopy.
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 2, 3
Description: Distribution of selected taxa for baseline versus follow-up
Abundance in Group 1: increased abundance in control group post-endoscopy
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-17
Source: Figure 3
Description: Distribution of selected taxa for baseline versus follow-up
Abundance in Group 1: decreased abundance in control group post-endoscopy
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae |
Revision editor(s): Jeshudy
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