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Research Article

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

  • Sahar Abubucker,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Nicola Segata,

    Affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

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  • Johannes Goll,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Alyxandria M. Schubert,

    Affiliation: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America

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  • Jacques Izard,

    Affiliations: Department of Molecular Genetics, Forsyth Institute, Cambridge, Massachusetts, United States of America, Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America

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  • Brandi L. Cantarel,

    Affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

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  • Beltran Rodriguez-Mueller,

    Affiliation: Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America

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  • Jeremy Zucker,

    Affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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  • Mathangi Thiagarajan,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Bernard Henrissat,

    Affiliation: Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Université de la Méditerranée, Marseille, France

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  • Owen White,

    Affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America

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  • Scott T. Kelley,

    Affiliation: Biology Department, San Diego State University, San Diego, California, United States of America

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  • Barbara Methé,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Patrick D. Schloss,

    Affiliation: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America

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  • Dirk Gevers,

    Affiliation: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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  • Makedonka Mitreva,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Curtis Huttenhower mail

    chuttenh@hsph.harvard.edu

    Affiliations: Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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About the Authors

Sahar Abubucker, Makedonka Mitreva
The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
Nicola Segata, Curtis Huttenhower
Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
Johannes Goll, Mathangi Thiagarajan, Barbara Methé
J. Craig Venter Institute, Rockville, Maryland, United States of America
Alyxandria M. Schubert, Patrick D. Schloss
Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
Jacques Izard
Department of Molecular Genetics, Forsyth Institute, Cambridge, Massachusetts, United States of America
Jacques Izard, Beltran Rodriguez-Mueller
Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
Brandi L. Cantarel, Owen White
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
Jeremy Zucker, Dirk Gevers, Curtis Huttenhower
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Bernard Henrissat
Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Université de la Méditerranée, Marseille, France
Scott T. Kelley
Biology Department, San Diego State University, San Diego, California, United States of America

Corresponding Author

Email: chuttenh@hsph.harvard.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: OW DG MM CH. Performed the experiments: SA AMS CH. Analyzed the data: SA NS AMS JI BLC CH. Contributed reagents/materials/analysis tools: JG BRM JZ MT BH STK BM PDS. Wrote the paper: SA NS CH. Implemented the software: NS BRM CH.