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

• Published in: Nature communications Vol. 9; no. 1; pp. 3347 - 12
• Main Authors: Takahashi, Melissa K., Tan, Xiao, Dy, Aaron J., Braff, Dana, Akana, Reid T., Furuta, Yoshikazu, Donghia, Nina, Ananthakrishnan, Ashwin, Collins, James J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21-08-2018; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/71; 38/88; 631/1647/1888; 631/326/2565/2134; 631/553/552; 692/699/255/1911; Biology; Biomarkers; Biomarkers - analysis; Clostridium difficile - genetics; Clostridium difficile - isolation & purification; Computational Biology; Correlation analysis; Cost analysis; Demand analysis; Feces - microbiology; Gastrointestinal Microbiome; Humanities and Social Sciences; Humans; Inflammation - pathology; Intestinal microflora; Longitudinal studies; Microbiomes; Microbiota; mRNA; multidisciplinary; Ribonucleic acid; RNA; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Ribosomal, 16S - genetics; Science; Science (multidisciplinary); Sensors; Species Specificity; Synthetic biology; Synthetic Biology - economics; Synthetic Biology - methods; Toxins
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-05864-4

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.
Currently, gut microbiome profiling largely relies on next-generation sequencing, which is slow and expensive. Here, the authors develop a low-cost, paper-based synthetic biology platform that allows species-specific quantification of bacterial mRNAs and clinically relevant host biomarkers.