Association between clinical and environmental factors and the gut microbiota profiles in young South African children/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Subjects
- Location of subjects
- South Africa
- 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
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group A (0-1 age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group B (>1 to 2 age)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with age group between > 1 to 2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5B
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).
Abundance in Group 1: increased abundance in Group B (>1 to 2 age)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Dorea | ||
| Faecalibacterium | ||
| Haemophilus | ||
| Lachnospiraceae bacterium NK4A136 | ||
| unclassified Lachnospiraceae |
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-19
Source: Figure 5B
Description: Statistically significant taxa identified by ANCOM labelled in the Comparison between groups A (0-1 age) & B (>1 to 2 age).
Abundance in Group 1: decreased abundance in Group B (>1 to 2 age)
| NCBI | Quality Control | Links |
|---|---|---|
| [Clostridium] innocuum |
Revision editor(s): Tosin
