Abstract Functional metagenomics is an attractive culture‐independent approach for functional screening of diverse microbiomes to identify known and novel genes. Since functional screening can involve sifting through tens of thousands of metagenomic library clones, an easy high‐throughput screening approach is desirable. Here, we demonstrate a proof‐of‐concept application of a low‐cost, high‐throughput droplet based microfluidic assay to the selection of antibiotic resistance genes from a soil metagenomic library. Metagenomic library members encapsulated in nanoliter volume water‐in‐oil droplets were printed on glass slides robotically, and cell growth in individual drops in the presence of ampicillin was imaged and quantified to identify ampicillin‐resistant clones. From the hits, true positives were confirmed by sequencing and functional validation. The ease of liquid handling, ease of set‐up, low cost, and robust workflow makes the droplet‐based nano‐culture platform a promising candidate for screening and selection assays for functional metagenomic libraries.
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