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

Edited by Daniel L. Hartl, Harvard University, Cambridge, MA, and approved June 30, 2010 (received for review April 29, 2010)
August 2, 2010
107 (33) 14691-14696

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.

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Data Availability

Data deposition: Data were submitted to the Sequence Read Archive (SRA) using ISA tools (ISAcreator and ISAconverter, http://isatab.sourceforge.net/index.html). The dataset is available at http://www.ebi.ac.uk/ena/data/view/ERP000133.

Acknowledgments

We thank the volunteers for their participation, G. Capponi from St. Camille Hospital and Solange Zemba from Nanoro (Burkina Faso), L. Turbanti (Centro Interdipartimentale di Spettrometria di Massa) and A.P. Femia (Department of Pharmacology) at the University of Florence, and P. Rocca Serra (EMBL-EBI) for assistance. This work was supported by Ministero dell'Istruzione, dell'Università e della Ricerca, Italy Grant PRIN 2007-N352CP_001, Ente Cassa di Risparmio di Firenze Grant 0875, and Meyer's Children Hospital.

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 107 | No. 33
August 17, 2010
PubMed: 20679230

Classifications

Data Availability

Data deposition: Data were submitted to the Sequence Read Archive (SRA) using ISA tools (ISAcreator and ISAconverter, http://isatab.sourceforge.net/index.html). The dataset is available at http://www.ebi.ac.uk/ena/data/view/ERP000133.

Submission history

Published online: August 2, 2010
Published in issue: August 17, 2010

Keywords

  1. metagenomics
  2. nutrigenomics
  3. biodiversity
  4. 454-pyrosequencing
  5. short-chain fatty acids

Acknowledgments

We thank the volunteers for their participation, G. Capponi from St. Camille Hospital and Solange Zemba from Nanoro (Burkina Faso), L. Turbanti (Centro Interdipartimentale di Spettrometria di Massa) and A.P. Femia (Department of Pharmacology) at the University of Florence, and P. Rocca Serra (EMBL-EBI) for assistance. This work was supported by Ministero dell'Istruzione, dell'Università e della Ricerca, Italy Grant PRIN 2007-N352CP_001, Ente Cassa di Risparmio di Firenze Grant 0875, and Meyer's Children Hospital.

Notes

*This Direct Submission article had a prearranged editor.

Authors

Affiliations

Carlotta De Filippo
Department of Preclinical and Clinical Pharmacology, University of Florence, 50139 Firenze, Italy;
Duccio Cavalieri
Department of Preclinical and Clinical Pharmacology, University of Florence, 50139 Firenze, Italy;
Monica Di Paola
Department of Pediatrics, Meyer Children Hospital, University of Florence, 50139 Firenze, Italy;
Matteo Ramazzotti
Department of Biochemical Sciences, University of Florence, 50134 Firenze, Italy;
Jean Baptiste Poullet
DNA Vision Agrifood S.A., B-4000 Liège, Belgium; and
Sebastien Massart
DNA Vision Agrifood S.A., B-4000 Liège, Belgium; and
Silvia Collini
Department of Pediatrics, Meyer Children Hospital, University of Florence, 50139 Firenze, Italy;
Giuseppe Pieraccini
Centro Interdipartimentale di Spettrometria di Massa, University of Florence, 50139 Firenze, Italy
Paolo Lionetti1 [email protected]
Department of Pediatrics, Meyer Children Hospital, University of Florence, 50139 Firenze, Italy;

Notes

1
To whom correspondence should be addressed. E-mail: [email protected].
Author contributions: C.D.F., D.C., and P.L. designed research; C.D.F., M.D.P., S.M., and S.C. performed research; G.P. contributed new reagents/analytic tools; M.R. and J.B.P. analyzed data; and C.D.F., D.C., M.D.P., and P.L. wrote the paper.

Competing Interests

The authors declare no conflict of interest.

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    Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
    Proceedings of the National Academy of Sciences
    • Vol. 107
    • No. 33
    • pp. 14515-14937

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