Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses/Experiment 1
Curated date: 2024/03/18
Curator: Aishat
Revision editor(s): WikiWorks, Scholastica, Victoria, Aishat, Ifeanyisam, Taofeecoh
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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants who are HIV unexposed and uninfected (iHUU) at week 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants who are HIV exposed but uninfected (iHEU) at week 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants at 1 week of age born to mothers from South Africa who have HIV but are not themselves infected with HIV
- 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
- 61
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).
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2
Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa
Abundance in Group 1: increased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 1
Revision editor(s): Aishat, Scholastica, WikiWorks
Signature 2
Source: Table 2
Description: Differentially abundant ASVs (adj P < 0.05) among iHEU (infants who are HIV exposed but uninfected) relative to iHUU (infants who are HIV unexposed and uninfected) at 1 week of age in South Africa
Abundance in Group 1: decreased abundance in Infants who are HIV exposed but uninfected (iHEU) at week 1
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Actinomyces | ||
| Parabacteroides distasonis |
Revision editor(s): Aishat, Scholastica, WikiWorks
