Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P
Journal
Proceedings of the National Academy of Sciences of the United States of America
Year
2010
Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Curated date: 2022/07/17
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Atrayees, ChiomaBlessing
Subjects
- Location of subjects
- Burkina Faso
- Italy
- 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
- Ethnic group , Place of residence measurement Ethnicity,race,Ethnic group,ethnic group,Place of residence measurement,place of residence measurement
- 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
- Statistical test
- Kruskall-Wallis
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Curated date: 2022/07/17
Curator: Kaluifeanyi101
Revision editor(s): Kaluifeanyi101, Atrayees, ChiomaBlessing
Source: Supporting Info. Table S5 + Fig. S2
Description: Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier
Abundance in Group 1: increased abundance in Rural African Children in Burkina Faso
Revision editor(s): Kaluifeanyi101, Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Source: Supporting Info. Table S5 + Fig. S2
Description: Report of the species assignment for BF and EU populations relative to the most abundant bacterial genera found by the RDP classifier
Abundance in Group 1: decreased abundance in Rural African Children in Burkina Faso
Revision editor(s): Kaluifeanyi101, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ethnic group , Place of residence measurement Ethnicity,race,Ethnic group,ethnic group,Place of residence measurement,place of residence measurement
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Source: Figure 3B
Description: 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 |
|---|---|---|
| Escherichia | ||
| Shigella |
Revision editor(s): Atrayees, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Source: Supporting Info. Fig. S1
Description: Boxplots (percentage of sequences) of the four most represented phyla in the BF compared to EU children.
Abundance in Group 1: increased abundance in Rural African Children in Burkina Faso
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidia |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Source: Supporting Info. Fig. S1
Description: Boxplots (percentage of sequences) of the four most represented phyla in the BF compared to EU children.
Abundance in Group 1: decreased abundance in Rural African Children in Burkina Faso
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Pseudomonadota |
Revision editor(s): ChiomaBlessing
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