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A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers

Author

Listed:
  • Melissa K. Takahashi

    (Massachusetts Institute of Technology)

  • Xiao Tan

    (Massachusetts Institute of Technology
    Massachusetts General Hospital
    Harvard Medical School
    Harvard University)

  • Aaron J. Dy

    (Massachusetts Institute of Technology
    Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

  • Dana Braff

    (Massachusetts Institute of Technology
    Boston University)

  • Reid T. Akana

    (Massachusetts Institute of Technology)

  • Yoshikazu Furuta

    (Massachusetts Institute of Technology
    Hokkaido University)

  • Nina Donghia

    (Harvard University)

  • Ashwin Ananthakrishnan

    (Massachusetts General Hospital
    Harvard Medical School)

  • James J. Collins

    (Massachusetts Institute of Technology
    Harvard University
    Broad Institute of MIT and Harvard
    Massachusetts Institute of Technology)

Abstract

There is a need for large-scale, longitudinal studies to determine the mechanisms by which the gut microbiome and its interactions with the host affect human health and disease. Current methods for profiling the microbiome typically utilize next-generation sequencing applications that are expensive, slow, and complex. Here, we present a synthetic biology platform for affordable, on-demand, and simple analysis of microbiome samples using RNA toehold switch sensors in paper-based, cell-free reactions. We demonstrate species-specific detection of mRNAs from 10 different bacteria that affect human health and four clinically relevant host biomarkers. We develop a method to quantify mRNA using our toehold sensors and validate our platform on clinical stool samples by comparison to RT-qPCR. We further highlight the potential clinical utility of the platform by showing that it can be used to rapidly and inexpensively detect toxin mRNA in the diagnosis of Clostridium difficile infections.

Suggested Citation

  • Melissa K. Takahashi & Xiao Tan & Aaron J. Dy & Dana Braff & Reid T. Akana & Yoshikazu Furuta & Nina Donghia & Ashwin Ananthakrishnan & James J. Collins, 2018. "A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05864-4
    DOI: 10.1038/s41467-018-05864-4
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    Cited by:

    1. Zhijin Tian & Dandan Shao & Linlin Tang & Zhen Li & Qian Chen & Yongxiu Song & Tao Li & Friedrich C. Simmel & Jie Song, 2024. "Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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