Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Subjects
- Location of subjects
- Taiwan
- 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
- Intestinal polyp intestinal polyp,intestinal polyp (disease),Intestinal Polyps,Polyp, Intestinal,Polyps, Intestinal,Intestinal polyp
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- polyps patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persons aged 25–95 years old with cancerous large intestine tumor symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- 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
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Metastats
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description: The post hoc plots of enriched bacterial genera among three health conditions (healthy, polyps, and cancer). The left side of these figures shows the abundance ratio of differentially enriched bacterial genera. The right side represents the significant difference at p < 0.05, whereas the middle one indicates the mean proportion of differentially enriched bacterial genera in the 95% confidence interval.
Abundance in Group 1: increased abundance in cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Campylobacter | ||
| Enterococcus | ||
| Slackia | ||
| Pyramidobacter | ||
| Coriobacterium | ||
| Methanobrevibacter | ||
| Peptostreptococcus | ||
| Abiotrophia | ||
| Coxiella | ||
| Haloferula | ||
| Leuconostoc | ||
| Weissella |
Revision editor(s): Chloe
Signature 2
Reviewed Marked as Reviewed by Chloe on 2023-3-8
Source: Figure 4
Description:
Abundance in Group 1: decreased abundance in cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonas | ||
| Sporobacterium | ||
| Oscillospira | ||
| Mitsuokella | ||
| Streptobacillus |
Revision editor(s): Chloe
