Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children under 5 years with Acute(AD) and Prolonged or persistent diarrhea(ProPD)
- 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
- 650
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, education level, 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
Source: Supplementary Table 1
Description: This is a box plot that compares the relative abundance of bacterial taxa in Ethiopian children with diarrhea (both acute and prolonged/persistent) to that in non-diarrheal controls.
Abundance in Group 1: increased abundance in Diarrhea
Revision editor(s): Cateline Ouma, Peace Sandy
Signature 2
Source: Figure 4a, Supplementary Table 1
Description: This is a box plot that shows the differential abundance between children with diarrhea (AD and ProPD) and healthy controls.
Abundance in Group 1: decreased abundance in Diarrhea
Revision editor(s): Cateline Ouma, Peace Sandy
Experiment 2
Subjects
- 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
- Acute Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children under 5 years with acute diarrhea that lasted less than 7 days prior to enrollment into the study
- Group 1 sample size Number of subjects in the case (exposed) group
- 554
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 4b, Supplementary Table 2
Description: A box plot comparing the relative abundance of taxa in children with acute diarrhea (AD) and non-diarrheal controls
Abundance in Group 1: increased abundance in Acute Diarrhea
Revision editor(s): Cateline Ouma, Peace Sandy
Signature 2
Source: Figure 4b, Supplementary Table 2
Description: A box plot comparing the relative abundance of taxa in children with acute diarrhea (AD) and non-diarrheal controls
Abundance in Group 1: decreased abundance in Acute Diarrhea
Revision editor(s): Cateline Ouma, Peace Sandy
Experiment 3
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
Statistical Analysis
- 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
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
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
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute Diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Combined cases of prolonged diarrhea (7-13 days) and persistent diarrhea (≥14 days)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 554
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, time, breast feeding, education level, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 4d, Supplementary Table 4
Description: A box plot showing differential abundance of taxa in ProPD cases versus AD cases.
Abundance in Group 1: increased abundance in Prolonged or Persistent Diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lactobacillus |
Revision editor(s): Cateline Ouma
Signature 2
Source: Figure 4d, Supplementary Table 4
Description: A box plot comparing the relative abundance of taxa in ProPD cases versus AD cases
Abundance in Group 1: decreased abundance in Prolonged or Persistent Diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes hadrus | ||
| Faecalibacterium prausnitzii | ||
| unclassified Coriobacteriaceae | ||
| unclassified Bacteroides |
Revision editor(s): Cateline Ouma, Peace Sandy
