Dietary intervention impact on gut microbial gene richness (original) (raw)

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Accessions

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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Acknowledgements

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

  1. Aurélie Cotillard, Sean P. Kennedy, Ling Chun Kong, Edi Prifti and Nicolas Pons: These authors contributed equally to this work.
  2. Commissariat à l’Energie Atomique, Genoscope, Evry 91000, France.

Authors and Affiliations

  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. Institut National de la Recherche Agronomique, Mathématiques et Informatique Appliquées, Jouy en Josas 78350, France.,
    Jean-Pierre Gauchi
  11. Institut National de la Recherche Agronomique, Mathématique, Informatique et Génome, Jouy en Josas 78350, France.,
    Jean-François Gibrat, Valentin Loux & Wilfrid Carré

Authors

  1. Aurélie Cotillard
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  2. Sean P. Kennedy
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  3. Ling Chun Kong
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  4. Edi Prifti
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  5. Nicolas Pons
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  6. Emmanuelle Le Chatelier
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  7. Mathieu Almeida
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  8. Benoit Quinquis
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  9. Florence Levenez
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  10. Nathalie Galleron
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  11. Sophie Gougis
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  12. Salwa Rizkalla
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  13. Jean-Michel Batto
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  14. Pierre Renault
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  15. Joel Doré
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  16. Jean-Daniel Zucker
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  17. Karine Clément
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  18. Stanislav Dusko Ehrlich
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Consortia

ANR MicroObes consortium

ANR MicroObes consortium members

Contributions

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.

Corresponding authors

Correspondence toKarine Clément or Stanislav Dusko Ehrlich.

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The authors declare no competing financial interests.

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Cotillard, A., Kennedy, S., Kong, L. et al. Dietary intervention impact on gut microbial gene richness.Nature 500, 585–588 (2013). https://doi.org/10.1038/nature12480

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