Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition/Experiment 2
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Reviewed Marked as Reviewed by Svetlana up on 2024-6-18
Curated date: 2024/03/23
Curator: Ehi
Revision editor(s): WikiWorks, Deacme, Scholastica, Victoria, Ehi, Ifeanyisam
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
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean female subjects in Bushbuckridge
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean female subjects in Soweto
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Lean females subjects living in Soweto whose microbiota was studied to understand transitional microbiome differences between subjects in Bushbuckridge and those in Soweto.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
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).
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-18
Source: Figure 5b and Supplementary Table 2B
Description: Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.
Abundance in Group 1: increased abundance in Lean female subjects in Soweto
Revision editor(s): WikiWorks, Deacme, Scholastica, Ehi
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-18
Source: Figure 5b and Supplementary Table 2B
Description: Phylum and Genus level significant differences between lean groups in the Bushbuckridge and Soweto cohorts.
Abundance in Group 1: decreased abundance in Lean female subjects in Soweto
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroides | ||
| Bacteroidota | ||
| Dialister | ||
| Pseudomonadota |
