• A Corrigendum to this article was published on 23 October 2013


Complex gene–environment interactions are considered important in the development of obesity1. The composition of the gut microbiota can determine the efficacy of energy harvest from food2,3,4 and changes in dietary composition have been associated with changes in the composition of gut microbial populations5,6. The capacity to explore microbiota composition was markedly improved by the development of metagenomic approaches7,8, which have already allowed production of the first human gut microbial gene catalogue9 and stratifying individuals by their gut genomic profile into different enterotypes10, but the analyses were carried out mainly in non-intervention settings. To investigate the temporal relationships between food intake, gut microbiota and metabolic and inflammatory phenotypes, we conducted diet-induced weight-loss and weight-stabilization interventions in a study sample of 38 obese and 11 overweight individuals. Here we report that individuals with reduced microbial gene richness (40%) present more pronounced dys-metabolism and low-grade inflammation, as observed concomitantly in the accompanying paper11. Dietary intervention improves low gene richness and clinical phenotypes, but seems to be less efficient for inflammation variables in individuals with lower gene richness. Low gene richness may therefore have predictive potential for the efficacy of intervention.

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European Nucleotide Archive

Data deposits

The raw solid read data for all samples has been deposited in the European Bioinformatics Institute (EBI) European Nucleotide Archive (ENA) under the accession number ERP003699.


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We are grateful to O. Pedersen (Univ. Copenhagen) for helpful comments on this manuscript and to the MetaHIT consortium for providing the gene profiles of the Danish subjects used to test the ROC models in advance of publication and the DNA samples sequenced on the SOLiD platform for comparison with the Illumina platform used in the accompanying manuscript. We thank C. Baudoin, P. Ancel and V. Pelloux who contributed to the clinical investigation study; S. Fellahi and J.-P. Bastard for analyses of inflammatory markers; D. Bonnefont-Rousselot and R. Bittar for help with the analysis of plasma lipid profile. This work was supported by Agence Nationale de la Recherche (ANR MICRO-Obes, ANR, Nutra2sens, ANR-10-IAHU-05), the Metagenopolis grant ANR-11-DPBS-0001, KOT-Ceprodi (Florence Massiera), Danone Research (Damien Paineau) and the associations Fondacoeur, and Louis-Bonduelle. Additional funding came from the European Commission FP7 grant HEALTH-F4-2007-201052 and METACARDIS.

Author information

Author notes

    • Aurélie Cotillard
    • , Sean P. Kennedy
    • , Ling Chun Kong
    • , Edi Prifti
    •  & Nicolas Pons

    These authors contributed equally to this work.


  1. Institut National de la Santé et de la Recherche Médicale, U872, Nutriomique, Équipe 7, Centre de Recherches des Cordeliers, Paris 75006, France

    • Aurélie Cotillard
    • , Ling Chun Kong
    • , Edi Prifti
    • , Salwa Rizkalla
    • , Jean-Daniel Zucker
    •  & Karine Clément
  2. Université Pierre et Marie-Curie-Paris 6, Nutriomique, 15 rue de l’Ecole de Medecine, Paris 75006, France

    • Aurélie Cotillard
    • , Ling Chun Kong
    • , Edi Prifti
    • , Salwa Rizkalla
    • , Jean-Daniel Zucker
    •  & Karine Clément
  3. INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas78350, France

    • Sean P. Kennedy
    • , Edi Prifti
    • , Nicolas Pons
    • , Emmanuelle Le Chatelier
    • , Mathieu Almeida
    • , Benoit Quinquis
    • , Florence Levenez
    • , Nathalie Galleron
    • , Jean-Michel Batto
    • , Joel Doré
    •  & Stanislav Dusko Ehrlich
  4. Institute of Cardiometabolism and Nutrition, Assistance Publique-Hôpitaux de Paris, CRNH-Ile de France, Pitié-Salpêtrière, Boulevard de l'Hopital, Paris 75013, France

    • Ling Chun Kong
    • , Sophie Gougis
    • , Salwa Rizkalla
    •  & Karine Clément
  5. INRA, Institut National de la Recherche Agronomique, UMR 1319 Micalis, Jouy en Josas 78350, France

    • Florence Levenez
    • , Jean-Michel Batto
    • , Pierre Renault
    •  & Joel Doré
  6. Institut de Recherche pour le Développement, IRD, UMI 209, UMMISCO, France Nord, Bondy F-93143, France

    • Jean-Daniel Zucker
  7. INRA, Institut National de la Recherche Agronomique, UMR 1319 Micalis, Jouy en Josas 78350, France.

    • Hervé Blottière
    • , Marion Leclerc
    • , Catherine Juste
    • , Tomas de Wouters
    • , Patricia Lepage
    • , Charlene Fouqueray
    • , Emmanuelle Maguin
    • , Maarten van de Guchte
    • , Alexandre Jamet
    • , Fouad Boumezbeur
    •  & Séverine Layec
  8. INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas 78350, France.

    • Hervé Blottière
  9. Institute of Cardiometabolism and Nutrition, Assistance Publique-Hôpitaux de Paris, CRNH-Ile de France, Pitié-Salpêtrière, Paris 75013, France.

    • Arnaud Basdevant
    • , Cornelieu Henegar
    • , Cindy Godard
    • , Marine Fondacci
    • , Alili Rohia
    •  & Froogh Hajduch
  10. Commissariat à l’Energie Atomique, Genoscope, Evry 91000, France.

  11. Institut National de la Recherche Agronomique, Mathématiques et Informatique Appliquées, Jouy en Josas 78350, France.

    • Jean-Pierre Gauchi
  12. Institut National de la Recherche Agronomique, Mathématique, Informatique et Génome, Jouy en Josas 78350, France.

    • Jean-François Gibrat
    • , Valentin Loux
    •  & Wilfrid Carré


  1. ANR MicroObes consortium

    A list of authors and affiliations appears at the end of the paper.

  2. ANR MicroObes consortium members


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S.D.E., J.D. and K.C. designed the study; S.D.E., J.D., K.C. and P.R. managed the study; K.C. and S.R. designed the clinical research; S.R. and L.C.K. conducted the clinical research and clinical data management; A.C., S.R. and L.C.K. conducted clinical and dietary data analysis; S.G. gave dietary counselling to the patients and carried out analysis of dietary data; F.L. prepared the DNA for sequencing; S.K. managed DNA sequencing, which B.Q. and N.G. carried out; N.P. and J.-M.B. established the sequence analysis pipeline; A.C., J.-D.Z., E.P., N.P., E.L.C., M.A., J.-M.B., S.K. and S.D.E. carried out microbial data analysis; A.C., K.C., L.C.K. and S.D.E. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Karine Clément or Stanislav Dusko Ehrlich.

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