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Micromachines 2017, 8(8), 230; doi:10.3390/mi8080230

A Droplet Microfluidics Based Platform for Mining Metagenomic Libraries for Natural Compounds

1
Metagenomix Inc., Branford, CT 06405, USA
2
Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
3
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
4
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
5
Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
6
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
*
Authors to whom correspondence should be addressed.
Received: 9 June 2017 / Revised: 14 July 2017 / Accepted: 19 July 2017 / Published: 25 July 2017
(This article belongs to the Special Issue Enabling Microfluidic Technologies for Single Cell Analysis)
View Full-Text   |   Download PDF [10544 KB, uploaded 25 July 2017]   |  

Abstract

Historically, microbes from the environment have been a reliable source for novel bio-active compounds. Cloning and expression of metagenomic DNA in heterologous strains of bacteria has broadened the range of potential compounds accessible. However, such metagenomic libraries have been under-exploited for applications in mammalian cells because of a lack of integrated methods. We present an innovative platform to systematically mine natural resources for pro-apoptotic compounds that relies on the combination of bacterial delivery and droplet microfluidics. Using the violacein operon from C. violaceum as a model, we demonstrate that E. coli modified to be invasive can serve as an efficient delivery vehicle of natural compounds. This approach permits the seamless screening of metagenomic libraries with mammalian cell assays and alleviates the need for laborious extraction of natural compounds. In addition, we leverage the unique properties of droplet microfluidics to amplify bacterial clones and perform clonal screening at high-throughput in place of one-compound-per-well assays in multi-well format. We also use droplet microfluidics to establish a cell aggregate strategy that overcomes the issue of background apoptosis. Altogether, this work forms the foundation of a versatile platform to efficiently mine the metagenome for compounds with therapeutic potential. View Full-Text
Keywords: metagenomic screening; droplet microfluidics; high-throughput screening; natural compound metagenomic screening; droplet microfluidics; high-throughput screening; natural compound
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Theodorou, E.; Scanga, R.; Twardowski, M.; Snyder, M.P.; Brouzes, E. A Droplet Microfluidics Based Platform for Mining Metagenomic Libraries for Natural Compounds. Micromachines 2017, 8, 230.

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