Issue 12, 2018

A universal platform for selection and high-resolution phenotypic screening of bacterial mutants using the nanowell slide

Abstract

The Petri dish and microtiter plate are the golden standard for selection and screening of bacteria in microbiological research. To improve on the limited resolution and throughput of these methods, we developed a universal, user-friendly platform for selection and high-resolution phenotypic screening based on the nanowell slide. This miniaturized platform has an optimal ratio between throughput and assay complexity, holding 672 nanowells of 500 nl each. As monoclonality is essential in bacterial genetics, we used FACS to inoculate each nanowell with a single bacterium in 15 min. We further extended the protocol to select and sort only bacteria of interest from a mixed culture. We demonstrated this by isolating single transposon mutants generated by a custom-made transposon with dual selection for GFP fluorescence and kanamycin resistance. Optical compatibility of the nanowell slide enabled phenotypic screening of sorted mutants by spectrophotometric recording during incubation. By processing the absorbance data with our custom algorithm, a phenotypic screen for growth-associated mutations was performed. Alternatively, by processing fluorescence data, we detected metabolism-associated mutations, exemplified by a screen for β-galactosidase activity. Besides spectrophotometry, optical compatibility enabled us to perform microscopic analysis directly in the nanowells to screen for mutants with altered morphologies. Despite the miniaturized format, easy transition from nano- to macroscale cultures allowed retrieval of bacterial mutants for downstream genetic analysis, demonstrated here by a cloning-free single-primer PCR protocol. Taken together, our FACS-linked nanowell slide replaces manual selection of mutants on agar plates, and enables combined selection and phenotypic screening in a one-step process. The versatility of the nanowell slide, and the modular workflow built on mainstream technologies, makes our universal platform widely applicable in microbiological research.

Graphical abstract: A universal platform for selection and high-resolution phenotypic screening of bacterial mutants using the nanowell slide

Supplementary files

Article information

Article type
Paper
Submitted
15 2 2018
Accepted
07 5 2018
First published
08 5 2018
This article is Open Access
Creative Commons BY-NC license

Lab Chip, 2018,18, 1767-1777

A universal platform for selection and high-resolution phenotypic screening of bacterial mutants using the nanowell slide

H. Antypas, M. Veses-Garcia, E. Weibull, H. Andersson-Svahn and A. Richter-Dahlfors, Lab Chip, 2018, 18, 1767 DOI: 10.1039/C8LC00190A

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