1
|
Nikolic N, Anagnostidis V, Tiwari A, Chait R, Gielen F. Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure. Front Microbiol 2023; 14:1260196. [PMID: 38075890 PMCID: PMC10703435 DOI: 10.3389/fmicb.2023.1260196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.
Collapse
Affiliation(s)
- Nela Nikolic
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
| | - Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Remy Chait
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
2
|
Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
Collapse
Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| |
Collapse
|
3
|
Medcalf EJ, Gantz M, Kaminski TS, Hollfelder F. Ultra-High-Throughput Absorbance-Activated Droplet Sorting for Enzyme Screening at Kilohertz Frequencies. Anal Chem 2023; 95:4597-4604. [PMID: 36848587 PMCID: PMC10018449 DOI: 10.1021/acs.analchem.2c04144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Droplet microfluidics is a valuable method to "beat the odds" in high throughput screening campaigns such as directed evolution, where valuable hits are infrequent and large library sizes are required. Absorbance-based sorting expands the range of enzyme families that can be subjected to droplet screening by expanding possible assays beyond fluorescence detection. However, absorbance-activated droplet sorting (AADS) is currently ∼10-fold slower than typical fluorescence-activated droplet sorting (FADS), meaning that, in comparison, a larger portion of sequence space is inaccessible due to throughput constraints. Here we improve AADS to reach kHz sorting speeds in an order of magnitude increase over previous designs, with close-to-ideal sorting accuracy. This is achieved by a combination of (i) the use of refractive index matching oil that improves signal quality by removal of side scattering (increasing the sensitivity of absorbance measurements); (ii) a sorting algorithm capable of sorting at this increased frequency with an Arduino Due; and (iii) a chip design that transmits product detection better into sorting decisions without false positives, namely a single-layered inlet to space droplets further apart and injections of "bias oil" providing a fluidic barrier preventing droplets from entering the incorrect sorting channel. The updated ultra-high-throughput absorbance-activated droplet sorter increases the effective sensitivity of absorbance measurements through better signal quality at a speed that matches the more established fluorescence-activated sorting devices.
Collapse
Affiliation(s)
- Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.,Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| |
Collapse
|
4
|
Wohlgemuth R, Littlechild J. Complexity reduction and opportunities in the design, integration and intensification of biocatalytic processes for metabolite synthesis. Front Bioeng Biotechnol 2022; 10:958606. [PMID: 35935499 PMCID: PMC9355135 DOI: 10.3389/fbioe.2022.958606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of metabolites from available starting materials is becoming an ever important area due to the increasing demands within the life science research area. Access to metabolites is making essential contributions to analytical, diagnostic, therapeutic and different industrial applications. These molecules can be synthesized by the enzymes of biological systems under sustainable process conditions. The facile synthetic access to the metabolite and metabolite-like molecular space is of fundamental importance. The increasing knowledge within molecular biology, enzyme discovery and production together with their biochemical and structural properties offers excellent opportunities for using modular cell-free biocatalytic systems. This reduces the complexity of synthesizing metabolites using biological whole-cell approaches or by classical chemical synthesis. A systems biocatalysis approach can provide a wealth of optimized enzymes for the biosynthesis of already identified and new metabolite molecules.
Collapse
Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, Zurich, Switzerland
- *Correspondence: Roland Wohlgemuth, ; Jennifer Littlechild,
| | - Jennifer Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Roland Wohlgemuth, ; Jennifer Littlechild,
| |
Collapse
|
5
|
Metabolic Engineering of Escherichia coli for Hyperoside Biosynthesis. Microorganisms 2022; 10:microorganisms10030628. [PMID: 35336203 PMCID: PMC8949062 DOI: 10.3390/microorganisms10030628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Hyperoside (quercetin 3-O-galactoside) exhibits many biological functions, along with higher bioactivities than quercetin. In this study, three UDP-dependent glycosyltransferases (UGTs) were screened for efficient hyperoside synthesis from quercetin. The highest hyperoside production of 58.5 mg·L−1 was obtained in a recombinant Escherichia coli co-expressing UGT from Petunia hybrida (PhUGT) and UDP-glucose epimerase (GalE, a key enzyme catalyzing the conversion of UDP-glucose to UDP-galactose) from E. coli. When additional enzymes (phosphoglucomutase (Pgm) and UDP-glucose pyrophosphorylase (GalU)) were introduced into the recombinant E. coli, the increased flux toward UDP-glucose synthesis led to enhanced UDP-galactose-derived hyperoside synthesis. The efficiency of the recombinant strain was further improved by increasing the copy number of the PhUGT, which is a limiting step in the bioconversion. Through the optimization of the fermentation conditions, the production of hyperoside increased from 245.6 to 411.2 mg·L−1. The production was also conducted using a substrate-fed batch fermentation, and the maximal hyperoside production was 831.6 mg·L−1, with a molar conversion ratio of 90.2% and a specific productivity of 27.7 mg·L−1·h−1 after 30 h of fermentation. The efficient hyperoside synthesis pathway described here can be used widely for the glycosylation of other flavonoids and bioactive substances.
Collapse
|
6
|
Yuan H, Tu R, Tong X, Lin Y, Zhang Y, Wang Q. OUP accepted manuscript. J Ind Microbiol Biotechnol 2022; 49:6544676. [PMID: 35259275 PMCID: PMC9142201 DOI: 10.1093/jimb/kuac007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/20/2022] [Indexed: 11/12/2022]
Abstract
Droplet-based microfluidics has emerged as a powerful tool for single-cell screening with ultrahigh throughput, but its widespread application remains limited by the accessibility of a droplet microfluidic high-throughput screening (HTS) platform, especially to common laboratories having no background in microfluidics. Here, we first developed a microfluidic HTS platform based on fluorescence-activated droplet sorting technology. This platform allowed (i) encapsulation of single cells in monodisperse water-in-oil droplets; (ii) cell growth and protein production in droplets; and (iii) sorting of droplets based on their fluorescence intensities. To validate the platform, a model selection experiment of a binary mixture of Bacillus strains was performed, and a 45.6-fold enrichment was achieved at a sorting rate of 300 droplets per second. Furthermore, we used the platform for the selection of higher α-amylase-producing Bacillus licheniformis strains from a mutant library generated by atmospheric and room temperature plasma mutagenesis, and clones displaying over 50% improvement in α-amylase productivity were isolated. This droplet screening system could be applied to the engineering of other industrially valuable strains.
Collapse
Affiliation(s)
| | | | - Xinwei Tong
- Shandong Longkete Enzyme Preparations Co., Ltd, Linyi 276400, China
| | - Yuping Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Yuanyuan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Qinhong Wang
- Correspondence should be addressed to: Qinhong Wang. Phone: +86-22-24821950. Fax: +86-22-24821950. E-mail:
| |
Collapse
|
7
|
Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
Collapse
Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| |
Collapse
|
8
|
Alex Wong CF, van Vliet L, Bhujbal SV, Guo C, Sletmoen M, Stokke BT, Hollfelder F, Lale R. A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalized Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution. ACS Synth Biol 2021; 10:1882-1894. [PMID: 34260196 PMCID: PMC8383311 DOI: 10.1021/acssynbio.1c00084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Water-in-oil emulsion
droplets are an attractive format for ultrahigh-throughput
screening in functional metagenomics and directed evolution applications
that allow libraries with more than 107 members to be characterized
in a day. Single library members are compartmentalized in droplets
that are generated in microfluidic devices and tested for the presence
of target biocatalysts. The target proteins can be produced intracellularly,
for example, in bacterial hosts in-droplet cell lysis is therefore
necessary to allow the enzymes to encounter the substrate to initiate
an activity assay. Here, we present a titratable lysis-on-demand (LoD)
system enabling the control of the cell lysis rate in Escherichia
coli. We demonstrate that the rate of cell lysis can be controlled
by adjusting the externally added inducer concentration. This LoD
system is evaluated both at the population level (by optical density
measurements) and at the single-cell level (on single-cell arrays
and in alginate microbeads). Additionally, we validate the LoD system
by droplet screening of a phosphotriesterase expressed from E. coli, with cell lysis triggered by inducer concentrations
in the μM range. The LoD system yields sufficient release of
the intracellularly produced enzymes to bring about a detectable quantity
of product (measured by fluorescence in flow cytometry of double emulsions),
while leaving viable cells for the downstream recovery of the genetic
material.
Collapse
Affiliation(s)
- Che Fai Alex Wong
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Liisa van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Swapnil Vilas Bhujbal
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Chengzhi Guo
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marit Sletmoen
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Bjørn Torger Stokke
- Department of Physics, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Rahmi Lale
- Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| |
Collapse
|
9
|
Charon J, Manteca A, Innis CA. Using the Bacterial Ribosome as a Discovery Platform for Peptide-Based Antibiotics. Biochemistry 2019; 58:75-84. [PMID: 30372045 PMCID: PMC7615898 DOI: 10.1021/acs.biochem.8b00927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
Collapse
Affiliation(s)
- Justine Charon
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - Aitor Manteca
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - C. Axel Innis
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| |
Collapse
|
10
|
Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria. Sci Rep 2018; 8:13087. [PMID: 30166560 PMCID: PMC6117260 DOI: 10.1038/s41598-018-31263-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022] Open
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 for producers of antibiotics in miniaturized bioreactors in which diverse cell mixtures can be screened on the single cell level is a promising approach to find novel antimicrobial scaffolds.
Collapse
|