Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life/Experiment 8
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
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
- HIV mother to child transmission HIV MTCT,HIV mother to child transmission,hIV mother to child transmission
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not exclusively breastfed HIV-unexposed infants (HUU) at 28 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not exclusively breastfed (formula feeding) In utero-HIV exposed uninfected infants (HEU) at 28 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Unexposed Infants who had been on antibiotics and HIV-exposed uninfected infants that had not been on Bactrim after 28 weeks of birth were excluded
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Source: Figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of lif
Abundance in Group 1: increased abundance in Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Epulonipiscium | ||
| unclassified_E01-9C-26unclassified_E01-9C-26 | ||
| Klebsiella | ||
| Pasteurella |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Source: figure 2e
Description: Genera with significantly different relative abundances between HEU and HUU not exclusively (Excl.) breastfed at 28 weeks of life
Abundance in Group 1: decreased abundance in Not exclusively breastfed HIV-exposed uninfected infants (HEU) at 28 weeks
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella | ||
| Mobiluncus | ||
| Alistipes | ||
| Catenibacterium | ||
| Dialister | ||
| Finegoldia | ||
| Gemella | ||
| Peptococcus | ||
| Peptostreptococcus | ||
| Solobacterium | ||
| Sneathia |
Revision editor(s): Folakunmi
