Gut Dysbiosis and Abnormal Bile Acid Metabolism in Colitis-Associated Cancer/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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 cancer cell line CRC cell line,Colorectal cancer cell line,colorectal cancer cell line
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group at week 10 (C10 group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- C57BL/6mice aged 7 weeks were obtained from Beijing Huafukang Bioscience Co. Inc. and acclimatized 1 week before the experiment. Intraperitoneal injection of 10mg/kg azoxymethane(AOM) was applied to the AOM/DSS group. After seven days, the AOM/DSS group was given1.5% dextran sodium sulfate (DSS) in drinking water on days 8–13, 27–32, and 46–51, and each cycle of DSS treatment was followed by 14-day drinking water. This was to create the colitis-induced colorectal cancer (CAC) model in the mice. Group 1 is the mice that developed CAC and had their fecal sample collected before being euthanized on day 70 (week 10).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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
- LEfSe
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18
Source: Figure 4c
Description: The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group
Abundance in Group 1: decreased abundance in azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroidales | ||
| Bacteroidia | ||
| Clostridiaceae | ||
| Clostridium | ||
| Desulfovibrio | ||
| Lachnospiraceae incertae sedis | ||
| Odoribacter | ||
| Porphyromonadaceae | ||
| Rikenellaceae |
Revision editor(s): Yjung24, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18
Source: Figure 4c
Description: The LefSe analysis listed bacteria with significant differences at different levels in AD10 group vs C10 group
Abundance in Group 1: increased abundance in azoxymethane/dextran sodiumsulfate (AOM/DSS) group at week 10 (AD10 group)
Revision editor(s): Yjung24, ChiomaBlessing
