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

Abstract

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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Life in a rural village of Burkina Faso. (A) Village of Boulpon. (B) Traditional Mossi dwelling. (C) Map of Burkina Faso (modified from the United States ClA's World Factbook, 34). (D) Millet and sorghum (basic components of Mossi diet) grain and flour in typical bowls. (E) Millet and sorghum is ground into flour on a grinding stone to produce a thick porridge called Tô.

Fig. 2.

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. (C) Dendrogram obtained with complete linkage hierarchical clustering of the samples from BF and EU populations based on their genera. The subcluster located in the middle of the tree contains samples taken from the three youngest (1–2 y old) children of the BF group (16BF, 3BF, and 4BF) and two 1-y-old children of the EU group (2EU and 3EU). (D) Relative abundances (percentage of sequences) of the four most abundant bacterial phyla in each individual among the BF and EU children. Blue area in middle shows abundance of Actinobacteria, mainly represented by Bifidobacterium genus, in the five youngest EU and BF children. (E) Relative abundance (percentage of sequences) of Gram-negative and Gram-positive bacteria in each individual. Different distributions of Gram-negative and Gram-positive in the BF and EU populations reflect differences in the two most represented phyla, Bacteroidetes and Firmicutes.

Fig. 3.

SCFA-producing bacteria could help to prevent establishment of some potentially pathogenic intestinal bacteria. (A) Quantification of SCFAs in fecal samples from BF and EU populations by SPME-GC-MS. (B) 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).