Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria

Scientific Reports
Lisa MahlerMartin Roth

Abstract

The natural bacterial diversity is regarded as a treasure trove for natural products. However, accessing complex cell mixtures derived from environmental samples in standardized high-throughput screenings is challenging. Here, we present a droplet-based microfluidic platform for ultrahigh-throughput screenings able to directly harness the diversity of entire microbial communities. This platform combines extensive cultivation protocols in aqueous droplets starting from single cells or spores with modular detection methods for produced antimicrobial compounds. After long-term incubation for bacterial cell propagation and metabolite production, we implemented a setup for mass spectrometric analysis relying on direct electrospray ionization and injection of single droplets. Even in the presence of dense biomass we show robust detection of streptomycin on the single droplet level. Furthermore, we developed an ultrahigh-throughput screening based on a functional whole-cell assay by picoinjecting reporter cells into droplets. Depending on the survival of reporter cells, droplets were selected for the isolation of producing bacteria, which we demonstrated for a microbial soil community. The established ultrahigh-throughput screening fo...Continue Reading

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Citations

Jan 11, 2019·Chembiochem : a European Journal of Chemical Biology·Aleksa Stanišić, Hajo Kries
Nov 30, 2018·Journal of Industrial Microbiology & Biotechnology·Richard H Baltz
Apr 6, 2021·Frontiers in Cell and Developmental Biology·Hang DuXiaojun Han
Jul 16, 2021·Journal of Applied Microbiology·Jenifer OssaiMadan K Kharel
Dec 21, 2018·Analytical Chemistry·Dominik HaidasPetra S Dittrich
Sep 22, 2021·Analytical Chemistry·Beiyu HuWenbin Du

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Methods Mentioned

BETA
chip
Assay
fluorescence activated droplet sorting
chips
PCR

Software Mentioned

ARB parsimony
Macrogen
SINA
LioniX
R
SeqTrace
phansalker
RAxML

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