Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission/Experiment 5
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-10-15
Subjects
- Location of subjects
- Malta
- 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
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non Smokers (No)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ex-smokers (Ex)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Inflammatory Bowel Disease (IBD) who were ex-smokers (had stopped smoking for at least 6 months).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 63
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-15
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: increased abundance in Ex-smokers (Ex)
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola dorei | ||
| unclassified Lachnospiraceae | ||
| unclassified Bacteroides | ||
| unclassified Parasutterella | ||
| unclassified Faecalibacterium |
Revision editor(s): Samreen-19
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-15
Source: Appendix Table 9
Description: Differential abundance analysis for smoking behaviour
Abundance in Group 1: decreased abundance in Ex-smokers (Ex)
Revision editor(s): Samreen-19
