Gut microbiome development along the colorectal adenoma-carcinoma sequence/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Subjects
- Location of subjects
- Austria
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Advanced Colorectal Adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- colorectal adenoma patients The study was conducted both in participants of a health screening programme according to national screening recommendations for CRC49 as well as in patients with suspected CRC undergoing colonoscopy as part of the clinical workup at the Department of Internal Medicine, Oberndorf Hospital.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 55
- 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)
- 3 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4a
Description: Control versus advanced adenoma (n = 55 and 42).
Abundance in Group 1: increased abundance in Advanced Colorectal Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Paraprevotella clara | ||
| Phocaeicola dorei | ||
| Phocaeicola massiliensis |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/06/23
Source: Figure 4a
Description: Control versus advanced adenoma (n = 55 and 42).
Abundance in Group 1: decreased abundance in Advanced Colorectal Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis | ||
| Streptococcus mutans |
Revision editor(s): Jeshudy
