Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

20679230

DOI Digital object identifier for electronic documents.

10.1073/pnas.1005963107

URI

https://pubmed.ncbi.nlm.nih.gov/20679230/

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

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Curated date: 2022/07/17

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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

Statistical test

ANOVA

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

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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

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Eggerthella
Bacteroidia
Anaerotruncus
Gracilibacter
Guggenheimella
Megamonas
Oxobacter
Propionispira

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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

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Bacillota
Pseudomonadota
Acetitomaculum
Faecalibacterium
Roseburia
Subdoligranulum
Alistipes
Bacteroides

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Experiment 2

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Differences from previous experiment shown

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

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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

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Escherichia
Salmonella
Shigella
Klebsiella

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