Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-29
Subjects
- Location of subjects
- Ethiopia
- 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
- Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prolonged or Persistent Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A combination of children whose diarrhea lasted for 7-13 days (Prolonged Diarrhea) and those whose diarrhea lasted for 14 days or longer (Persistent Diarrhea).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 663
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
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).
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, time, region of residence, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, time, breast feeding, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-29
Source: Figure 4c, Supplementary table 3
Description: DESEq2 differential abundance of taxa in children with prolonged or persistent diarrhea (ProPD) and non-diarrheal controls.
Abundance in Group 1: increased abundance in Prolonged or Persistent Diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. | ||
| Limosilactobacillus mucosae | ||
| Veillonella dispar | ||
| unclassified Bacteria | ||
| unclassified Campylobacter | ||
| unclassified Streptococcus | ||
| Mediterraneibacter gnavus |
Revision editor(s): Cateline Ouma, Rahila
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-29
Curated date: 2024/10/11
Curator: Cateline Ouma
Revision editor(s): Cateline Ouma, Rahila, Peace Sandy
Source: Figure 4c, Supplementary table 3
Description: DESeq2 analysis of differentially abundant taxa
Abundance in Group 1: decreased abundance in Prolonged or Persistent Diarrhea
Revision editor(s): Cateline Ouma, Rahila, Peace Sandy
