Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
Subjects
- Location of subjects
- Chile
- 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
- Hypercholesterolemia Elevated serum cholesterol,Elevated total cholesterol,High cholesterol,Increased total cholesterol,Hypercholesterolemia,hypercholesterolemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normocholesterolemic individuals (controls)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- hypercholesterolemic (cases)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with hypercholesterolemia (concentration of LDL-C greater than 4.16mmol/L)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
Source: Figure 3
Description: Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05
Abundance in Group 1: decreased abundance in hypercholesterolemic (cases)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Selenomonas | ||
| Victivallis |
Revision editor(s): Abiola-Salako, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
Source: Figure 3
Description: Microbial taxa with Linear discriminant analysis (LDA) score greater than 2 present in hypercholesterolemic individuals (red) and controls (green). P-value <0.05.
Abundance in Group 1: increased abundance in hypercholesterolemic (cases)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Chromatiales | ||
| Coriobacteriaceae | ||
| Eubacteriales | ||
| Methanosphaera | ||
| Rothia |
Revision editor(s): Abiola-Salako, Folakunmi
