Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- 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
- Constipation Constipation,Costiveness,Dyschezia,constipation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Negative Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Constipation Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Constipation Group were Sprague–Dawley male rats that had a constipation-like phenotype induced by intragastrical administration of white vinegar and activated carbon-cold water for 5 weeks. The diagnostic Criteria are: 1. Longer gastrointestinal transit time: Rats with constipation-like phenotype took significantly longer to complete gastrointestinal propulsion compared to controls. 2. Reduced small intestinal propulsion rate: The propulsion rate of the small intestine was significantly lower in constipated rats. 3. Decreased defecation frequency and volume: The frequency and amount of defecation were significantly reduced, mimicking clinical constipation symptoms in humans.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Figures 2B and 2D
Description: Represents the LDA Effect Size (LEfSe) analysis results comparing the Negative Control and Constipation Group.
Abundance in Group 1: increased abundance in Constipation Group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Bilophila | ||
| Lachnospiraceae | ||
| Phascolarctobacterium | ||
| Ruminococcus | ||
| Veillonellaceae | ||
| RC4-4RC4-4 |
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Figures 2B and 2D
Description: Represents the LDA Effect Size (LEfSe) analysis results comparing the Negative Control and Constipation Group.
Abundance in Group 1: decreased abundance in Constipation Group
Revision editor(s): Thelee98, MyleeeA, KateRasheed
