Gut mucosal microbiome across stages of colorectal carcinogenesis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26
Curated date: 2022/06/24
Curator: Jeshudy
Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Peace Sandy
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 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
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colorectal adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- histology-proven adenoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V4
- 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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26
Source: Supplementary Figure 9
Description: Differential microbial abundance between patients with colorectal adenoma and controls
Abundance in Group 1: increased abundance in colorectal adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacteroides uniformis | ||
| Blautia sp. | ||
| Enhydrobacter sp. | ||
| Escherichia coli | ||
| Gemella sp. | ||
| Parvimonas sp. | ||
| Peptostreptococcus sp. | ||
| Prevotella intermedia |
Revision editor(s): Jeshudy, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26
Source: Supplementary Figure 9
Description: Differential microbial abundance between patients with colorectal adenoma and controls
Abundance in Group 1: decreased abundance in colorectal adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacteroides sp. | ||
| Bacteroides uniformis | ||
| Blautia obeum | ||
| Blautia sp. | ||
| Coprococcus sp. | ||
| Faecalibacterium prausnitzii | ||
| Prevotella sp. |
Revision editor(s): Jeshudy, Claregrieve1
