Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
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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
- Burkina Faso
- Italy
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- ethnic group , socioeconomic statusEthnicity,race,ethnic group,socioeconomic status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- European Children in Italy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rural African Children in Burkina Faso
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 14 healthy children (nine male and six female) living in the rural village of Boulpon district of Nanoro, Boulkiemde province, Burkina Faso.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V6
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2, Figure S2
Description: taxa that significantly differentiate between the two groups
Abundance in Group 1: increased abundance in Rural African Children in Burkina Faso
NCBI | Quality Control | Links |
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Eggerthella | ||
Bacteroidia | ||
Anaerotruncus | ||
Gracilibacter | ||
Guggenheimella | ||
Megamonas | ||
Oxobacter | ||
Propionispira |
Revision editor(s): Kaluifeanyi101, Atrayees
Signature 2
Source: Figure 2; Figure 3B
Description: Description: 16S rRNA gene surveys reveal a clear separation of two children populations investigated. (A and B) Pie charts of median values of bacterial genera present in fecal samples of BF and EU children (>3%) found by RDP classifier v. 2.1. Rings represent corresponding phylum (Bacteroidetes in green and Firmicutes in red) for each of the most frequently represented genera.
(Fig. 3B). Number of sequences relative to principal Enterobacteriaceae genera, in BF and EU children microbiota.
Abundance in Group 1: decreased abundance in Rural African Children in Burkina Faso
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Pseudomonadota | ||
Acetitomaculum | ||
Faecalibacterium | ||
Roseburia | ||
Subdoligranulum | ||
Alistipes | ||
Bacteroides |
Revision editor(s): Kaluifeanyi101
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- ethnic group Ethnicity,race,ethnic group
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- European children in Italy
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 3B
Description: Number of sequences relative to principal Enterobacteriaceae genera, in BF and EU children microbiota. Mean values (±SEM) are plotted. Asterisks indicate significant differences (one-tailed Student t test of all data points: *P < 0.05; **P ≤ 0.01; ***P ≤ 0.001).
Abundance in Group 1: decreased abundance in Rural African Children in Burkina Faso
NCBI | Quality Control | Links |
---|---|---|
Escherichia | ||
Salmonella | ||
Shigella | ||
Klebsiella |
Revision editor(s): Atrayees