Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

Derek Thibault, Paul A. Jensen, Stephen Wood, Christine Qabar, Stacie Clark, Mara G. Shainheit, Ralph R. Isberg and Tim van Opijnen ()
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Derek Thibault: Boston College
Paul A. Jensen: Boston College
Stephen Wood: Boston College
Christine Qabar: Towson University
Stacie Clark: Tufts University School of Medicine
Mara G. Shainheit: Towson University
Ralph R. Isberg: Tufts University School of Medicine
Tim van Opijnen: Boston College

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. Droplet Tn-Seq (dTn-Seq) solves this problem by microfluidics facilitated encapsulation of individual transposon mutants into growth medium-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Here we describe and validate microfluidic chip design, production, encapsulation, and dTn-Seq sample preparation. We determine that 1–3% of mutants in Streptococcus pneumoniae have a different fitness when grown in isolation and show how dTn-Seq can help identify leads for gene function, including those involved in hyper-competence, processing of alpha-1-acid glycoprotein, sensitivity against the human leukocyte elastase and microcolony formation. Additionally, we show dTn-Seq compatibility with microscopy, FACS and investigations of bacterial cell-to-cell and bacteria-host cell interactions. dTn-Seq reduces costs and retains the advantages of Tn-Seq, while expanding the method’s original applicability.

Date: 2019
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DOI: 10.1038/s41467-019-13719-9

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