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Current understanding of the human microbiome

Nature Medicine volume 24, pages 392400 (2018) | Download Citation

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Abstract

Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities that are associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes and by mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this review, we focus on studies in humans to describe these challenges and propose strategies that leverage existing knowledge to move rapidly from correlation to causation and ultimately to translation into therapies.

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  • 12 June 2018

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Acknowledgements

Many of the studies described here in our laboratories were supported by the National Institutes of Health, National Science Foundation, Department of Energy and the Alfred P. Sloan Foundation. We thank numerous members of our laboratories for constructive criticism on drafts of this article.

Author information

Affiliations

  1. Microbiome Center, Department of Surgery, University of Chicago, Chicago, Illinois, USA.

    • Jack A Gilbert
  2. Bioscience Division, Argonne National Laboratory, Lemont, Illinois, USA.

    • Jack A Gilbert
  3. Marine Biological Laboratory, Woods Hole, Massachusetts, USA.

    • Jack A Gilbert
  4. New York University Langone Medical Center, New York, New York, USA.

    • Martin J Blaser
  5. Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA.

    • J Gregory Caporaso
  6. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.

    • Janet K Jansson
  7. Department of Medicine, University of California San Francisco, San Francisco, California, USA.

    • Susan V Lynch
  8. Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.

    • Rob Knight
  9. Department of Computer Science & Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.

    • Rob Knight
  10. Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA.

    • Rob Knight

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Rob Knight.

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https://doi.org/10.1038/nm.4517

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