Droplet microfluidics for microbiology: techniques, applications and challenges

A microfluidic co-cultivation platform to investigate microbial interactions at defined microenvironments

Interspecies interactions inside microbial communities bear a tremendous diversity of complex chemical processes that are by far not understood. Even for simplified, often synthetic systems, the interactions between two microbes are barely revealed in detail. Here, we present a microfluidic co-cultivation platform for the analysis of growth and interactions inside microbial consortia with single-cell resolution. Our device allows the spatial separation of two different microbial organisms inside adjacent microchambers facilitating sufficient exchange of metabolites via connecting nanochannels. Inside the cultivation chambers cell growth can be observed with high spatio-temporal resolution by live-cell imaging. In contrast to conventional approaches, in which single-cell activity is typically fully masked by the average bulk behavior, the small dimensions of the microfluidic cultivation chambers enable accurate environmental control and observation of cellular interactions with full spatio-temporal resolution. Our method enables one to study phenomena in microbial interactions, such as gene transfer or metabolic cross-feeding. We chose two different microbial model systems to demonstrate the wide applicability of the technology. First, we investigated commensalistic interactions between an industrially relevant l-lysine-producing Corynebacterium glutamicum strain and an l-lysine auxotrophic variant of the same species. Spatially separated co-cultivation of both strains resulted in growth of the auxotrophic strain due to secreted l-lysine supplied by the producer strain. As a second example we investigated bacterial conjugation between Escherichia coli S17-1 and Pseudomonas putida KT2440 cells. We could show that direct cell contact is essential for the successful gene transfer via conjugation and was hindered when cells were spatially separated. The presented device lays the foundation for further studies on contactless and contact-based interactions of natural and synthetic microbial communities.

Controlling the distance of highly confined droplets in a capillary by interfacial tension for merging on-demand

Droplet microfluidics is a powerful technology that finds many applications in chemistry and biomedicine. Among different configurations, droplets confined in a capillary (or plugs) present a number of advantages: they allow positional identification and simplify the integration of complex multi-steps protocols. However, these protocols rely on the control of droplet speed, which is affected by a complex and still debated interplay of various physico-chemical parameters like droplet length, viscosity ratio between droplets and carrier fluid, flow rate and interfacial tension. We present here a systematic investigation of the droplet speed as a function of their length and interfacial tension, and propose a novel, simple and robust methodology to control the relative distance between consecutive droplets flowing in microfluidic channels through the addition of surfactants either into the dispersed and/or into the continuous phases. As a proof of concept application, we present the possibility to accurately trigger in space and time the merging of two confined droplets flowing in a uniform cross-section circular capillary. This approach is further validated by monitoring a conventional enzymatic reaction used to quantify the concentration of H2O2 in a biological sample, showing its potentialities in both continuous and stopped assay methods.

Adhesion of Marinobacter hydrocarbonoclasticus to Surfactant-Decorated Dodecane Droplets

We investigate the effect of interfacial properties on the adhesion of bacteria at oil/water interfaces using confocal microscopy. Surfactant-decorated dodecane droplets of diameter 20-60 μm are generated using a coflow microfluidic device, introduced into an aqueous saline suspension of Marinobacter hydrocarbonoclasticus bacteria, and imaged in 3-D over time. Using image analysis algorithms, we determine the number of bacteria adhering at oil/water interfaces over time in the presence of dioctyl sodium succinate (DOSS), a component of the dispersant used in oil-spill recovery. The adsorption of bacteria at the oil/water interface follows Langmuir first-order kinetics for all droplet sizes, with the greatest areal number density of bacteria adhered to the smallest droplets. We vary the surfactant type [DOSS, dicyclohexyl sodium sulfosuccinate, dibutyl sodium sulfosuccinate, cetyltrimethylammonium bromide, and Tween 20] and concentration and examine the effects on long-time adhesion of bacteria. For a fixed droplet size, the areal density of bacteria at the interface decreases with increasing surfactant concentration because of a reduction in oil/water interfacial tension that increases the free energy of adhesion of the bacterium.

Asymmetric Membrane for Digital Detection of Single Bacteria in Milliliters of Complex Water Samples

In this work, we introduce an asymmetric membrane as a simple and robust nanofluidic platform for digital detection of single pathogenic bacteria directly in 10 mL of unprocessed environmental water samples. The asymmetric membrane, consisting of uniform micropores on one side and a high density of vertically aligned nanochannels on the other side, was prepared within 1 min by a facile method. The single membrane covers all the processing steps from sample concentration, purification, and partition to final digital loop-mediated isothermal amplification (LAMP). By simple filtration, bacteria were enriched and partitioned inside the micropores, while inhibitors typically found in the environmental samples ( i.e., proteins, heavy metals, and organics) were washed away through the nanochannels. Meanwhile, large particles, indigenous plankton, and positively charged pollutants in the samples were excluded by using a sacrificial membrane stacked on top. After initial filtration, modified LAMP reagents, including NaF and lysozyme, were loaded onto the membrane. Each pore in the asymmetric membrane functioned as an individual nanoreactor for selective, rapid, and efficient isothermal amplification of single bacteria, generating a bright fluorescence for direct counting. Even though high levels of inhibitors were present, absolute quantification of Escherichia coli and Salmonella directly in an unprocessed environmental sample (seawater and pond water) was achieved within 1 h, with sensitivity down to single cell and a dynamic range of 0.3-10000 cells/mL. The simple and low-cost analysis platform described herein has an enormous potential for the detection of pathogens, exosomes, stem cells, and viruses as well as single-cell heterogeneity analysis in environmental, food, and clinical research.

Interfacial Emulsification: An Emerging Monodisperse Droplet Generation Method for Microreactors and Bioanalysis

The generation of uniform droplets has been extensively investigated owing to its profound potentials both in scientific research and engineering applications. Although various methods have been put forward to expand this area, new innovations are still needed to improve the technical convenience and save instrumental cost. In this feature article, we highlight an interfacial emulsification technique that we developed in the past several years. This technique serves as a platform for preparing uniform droplets that are formed on the air-liquid interface of the continuous phase based on interfacial shearing. Three specific aspects of interfacial emulsification are reviewed, including its basic design and principle, the preparation of droplets with controllable size and adjustable components, and practical applications of the method in bioanalysis, microreactors, and particle synthesis. Compared to other droplet generation methods, several attractive advantages and perspectives for further development have been summarized.

Continuous Recirculation of Microdroplets in a Closed Loop Tailored for Screening of Bacteria Cultures

Emerging microfluidic technology has introduced new precision controls over reaction conditions. Owing to the small amount of reagents, microfluidics significantly lowers the cost of carrying a single reaction. Moreover, in two-phase systems, each part of a dispersed fluid can be treated as an independent chemical reactor with a volume from femtoliters to microliters, increasing the throughput. In this work, we propose a microfluidic device that provides continuous recirculation of droplets in a closed loop, maintaining low consumption of oil phase, no cross-contamination, stabilized temperature, a constant condition of gas exchange, dynamic feedback control on droplet volume, and a real-time optical characterization of bacterial growth in a droplet. The channels (tubing) and junction cubes are made of Teflon fluorinated ethylene propylene (FEP) to ensure non-wetting conditions and to prevent the formation of biofilm, which is particularly crucial for biological experiments. We show the design and operation of a novel microfluidic loop with the circular motion of microdroplet reactors monitored with optical sensors and precision temperature controls. We have employed the proposed system for long term monitoring of bacterial growth during the antibiotic chloramphenicol treatment. The proposed system can find applications in a broad field of biomedical diagnostics and therapy.

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

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.

Direct Observation of Bacterial Growth in Giant Unilamellar Vesicles: A Novel Tool for Bacterial Cultures

Bacterial cultivation techniques are classic, basic, and common processes used to characterize the physiological activity of bacteria in their environment. Owing to recent advances in bacterial cultivation techniques, the physiological activity of bacteria can be elucidated at the single-cell culture level. Here, we report a novel method to monitor the real-time activity of bacterial growth at the single-cell level inside giant unilamellar vesicles (GUVs). This method consists of two steps: 1) encapsulation of single bacteria in 1-33 pL scale GUVs and 2) immobilization of the GUVs on a planar lipid bilayer membrane on a glass surface. We directly observed single E. coli cells actively growing to a great number of cells inside GUVs. GUVs also protected the bacteria from external antibiotic compounds during prolonged cultivation for more than 24 h. This approach can be applied widely in the fields of biochemistry, biotechnology, microbiology, and synthetic biology.

Fast selective trapping and release of picoliter droplets in a 3D microfluidic PDMS multi-trap system with bubbles

The selective manipulation and incubation of individual picoliter drops in high-throughput droplet based microfluidic devices still remains challenging. We used a surface acoustic wave (SAW) to induce a bubble in a 3D designed multi-trap polydimethylsiloxane (PDMS) device to manipulate multiple droplets and demonstrate the selection, incubation and on-demand release of aqueous droplets from a continuous oil flow. By controlling the position of the acoustic actuation, individual droplets are addressed and selectively released from a droplet stream of 460 drops per s. A complete trapping and releasing cycle can be as short as 70 ms and has no upper limit for incubation time. We characterize the fluidic function of the hybrid device in terms of electric power, pulse duration and acoustic path.

Simple and Precise Counting of Viable Bacteria by Resazurin-Amplified Picoarray Detection

Simple, fast, and precise counting of viable bacteria is fundamental to a variety of microbiological applications such as food quality monitoring and clinical diagnosis. To this end, agar plating, microscopy, and emerging microfluidic devices for single bacteria detection have provided useful means for counting viable bacteria, but they also have their limitations ranging from complexity, time, and inaccuracy. We present herein our new method RAPiD (Resazurin-Amplified Picoarray Detection) for addressing this important problem. In RAPiD, we employ vacuum-assisted sample loading and oil-driven sample digitization to stochastically confine single bacteria in Picoarray, a microfluidic device with picoliter-sized isolation chambers (picochambers), in <30 s with only a few minutes of hands-on time. We add AlamarBlue, a resazurin-based fluorescent dye for bacterial growth, in our assay to accelerate the detection of "microcolonies" proliferated from single bacteria within picochambers. Detecting fluorescence in picochambers as an amplified surrogate for bacterial cells allows us to count hundreds of microcolonies with a single image taken via wide-field fluorescence microscopy. We have also expanded our method to practically test multiple titrations from a single bacterial sample in parallel. Using this expanded "multi-RAPiD" strategy, we can quantify viable cells in E. coli and S. aureus samples with precision in ∼3 h, illustrating RAPiD as a promising new method for counting viable bacteria for microbiological applications.

Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes

With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa. Still, while most of these methods give immediate access to downstream whole genome sequencing, upscaling to higher cell densities as required for metabolic readouts and preservation purposes can remain challenging. Provided that these and other technological challenges are addressed in future innovation rounds, integration of single-cell tools in commercially available benchtop instruments and service platforms is expected to trigger more targeted explorations in the microbial dark matter at a depth comparable to metagenomics.

Improved experimental time of ultra-large bioassays using a parallelised microfluidic biochip architecture/scheduling

Digital microfluidic is an emerging technology to reduce the cost and time of experiments and improve the flexibility, automate-ability and correctness of biochemical assays. In many of applications such as drug discovery and DNA profiling, a large number of bio-operations (e.g. the chemical operations used in biology applications) must be done. In these applications, parallelising the operations will be critical in accuracy and cost of the process and digital microfluidic biochips can be considered as a reasonable platform. In this study, a new microfluidic architecture and the corresponding CAD flow is introduced to parallelise the assays on this platform. The authors implemented the proposed architecture and evaluated it using the large real bioassays. The authors' simulations show that the degree-of-parallelism and speed of bioassays are increased more than 4× and the improvements will be better for larger assays. This contribution can open new horizons in drug testing, biology experiments and medical diagnosis operations that contain iterative, time-consuming and labour experiments.

Accelerating bacterial growth detection and antimicrobial susceptibility assessment in integrated picoliter droplet platform

There remains an urgent need for rapid diagnostic methods that can evaluate antibiotic resistance for pathogenic bacteria in order to deliver targeted antibiotic treatments. Toward this end, we present a rapid and integrated single-cell biosensing platform, termed dropFAST, for bacterial growth detection and antimicrobial susceptibility assessment. DropFAST utilizes a rapid resazurin-based fluorescent growth assay coupled with stochastic confinement of bacteria in 20 pL droplets to detect signal from growing bacteria after 1h incubation, equivalent to 2-3 bacterial replications. Full integration of droplet generation, incubation, and detection into a single, uninterrupted stream also renders this platform uniquely suitable for in-line bacterial phenotypic growth assessment. To illustrate the concept of rapid digital antimicrobial susceptibility assessment, we employ the dropFAST platform to evaluate the antibacterial effect of gentamicin on E. coli growth.

Detection of viability of micro-algae cells by optofluidic hologram pattern

A rapid detection of micro-algae activity is critical for analysis of ship ballast water. A new method for detecting micro-algae activity based on lens-free optofluidic holographic imaging is presented in this paper. A compact lens-free optofluidic holographic imaging device was developed. This device is mainly composed of a light source, a small through-hole, a light propagation module, a microfluidic chip, and an image acquisition and processing module. The excited light from the light source passes through a small hole to reach the surface of the micro-algae cells in the microfluidic chip, and a holographic image is formed by the diffraction light of surface of micro-algae cells. The relation between the characteristics in the hologram pattern and the activity of micro-algae cells was investigated by using this device. The characteristics of the hologram pattern were extracted to represent the activity of micro-algae cells. To demonstrate the accuracy of the presented method and device, four species of micro-algae cells were employed as the test samples and the comparison experiments between the alive and dead cells of four species of micro-algae were conducted. The results show that the developed method and device can determine live/dead microalgae cells accurately.

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we developed a 3D-printed, low-cost droplet microfluidic control instrument and deploy it in a clinical environment to perform single-cell transcriptome profiling of disaggregated synovial tissue from five rheumatoid arthritis patients. We sequence 20,387 single cells revealing 13 transcriptomically distinct clusters. These encompass an unsupervised draft atlas of the autoimmune infiltrate that contribute to disease biology. Additionally, we identify previously uncharacterized fibroblast subpopulations and discern their spatial location within the synovium. We envision that this instrument will have broad utility in both research and clinical settings, enabling low-cost and routine application of microfluidic techniques.

Droplet-based single-cell RNA-seq is a powerful tool for cellular heterogeneity profiling in disease but is limited by instrumentation required. Here the authors develop a 3D printed microfluidic platform for massive parallel sequencing of rheumatoid arthritis tissues.

Continuous splitting of aqueous droplets at the interface of co-flowing immiscible oil streams in a microchannel

We report the continuous splitting of aqueous droplets at the interface between two co-flowing immiscible oil streams in a microchannel. The aqueous droplets initially present in a primary continuous stream (CP₁) migrate into a secondary continuous stream (CP₂) when the ratio of the non-inertial lift force to the interfacial tension force exceeds a critical value (K. S. Jayaprakash, U. Banerjee and A. K. Sen, Langmuir, 2016, 32, 2136-2143). Here, experiments were performed to understand the droplet splitting phenomenon and demonstrate the splitting of droplets encapsulating microbeads and cells. The results showed that the droplet splitting phenomenon is governed by the capillary number Ca, which is a function of the average shear stress across the channel, interfacial tension σ between the CP₁ and the droplet phase and the droplet length-scale L. Irrespective of the individual values of these parameters, droplet splitting was observed when the capillary number Ca exceeds a critical value Ca_cr, which was found to be a function of droplet to CP₂ viscosity ratio λ. The Ca_cr was found to be minimum for λ ≈ 1 but higher for droplets of λ ≫ 1 and λ ≪ 1. The sizes of the primary and secondary daughter and migrated droplets (i.e. L_p|sD and L_p|sM) were found to increase linearly with the increase in the size of the primary or secondary parent droplets (L_p|sP). Splitting of parent droplets encapsulating a single microbead or PBMC showed that after splitting, the presence of the microbead or PBMC in the daughter or migrated droplets depends on the ratio of the size of the migrated droplets to that of the parent droplet (i.e. V_M/V_P). Finally, splitting of parent droplets containing two or more microbeads or cells into droplets containing a single particle or cell was demonstrated. A new paradigm of droplet splitting is reported that could find applications in soft matter and single-cell studies.

Polydisperse emulsion digital assay to enhance time to detection and extend dynamic range in bacterial cultures enabled by a statistical framework

We have developed a simple method for preparing small-volume droplets for performing digital culture, allowing for the detection of bacteria.

Simulation before fabrication: a case study on the utilization of simulators for the design of droplet microfluidic networks

The functional performance of passively operated droplet microfluidics is sensitive with respect to the dimensions of the channel network, the fabrication precision as well as the applied pressure because the entire network is coupled together. Especially, the local and global hydrodynamic resistance changes caused by droplets make the task to develop a robust microfluidic design challenging as plenty of interdependencies which all affect the intended behavior have to be considered by the designer. After the design, its functionality is usually validated by fabricating a prototype and testing it with physical experiments. In case that the functionality is not implemented as desired, the designer has to go back, revise the design, and repeat the fabrication as well as experiments. This current design process based on multiple iterations of refining and testing the design produces high costs (financially as well as in terms of time). In this work, we show how a significant amount of those costs can be avoided when applying simulation before fabrication. To this end, we demonstrate how simulations on the 1D circuit analysis model can help in the design process by means of a case study. Therefore, we compare the design process with and without using simulation. As a case study, we use a microfluidic network which is capable of trapping and merging droplets with different content on demand. The case study demonstrates how simulation can help to validate the derived design by considering all local and global hydrodynamic resistance changes. Moreover, the simulations even allow further exploration of different designs which have not been considered before due to the high costs.

Simulating microfluidic networks allows to check a design even before first prototypes are realized.

Particle Manipulation Methods in Droplet Microfluidics

This Feature describes the different particle manipulation techniques available in the droplet microfluidics toolbox to handle particles encapsulated inside droplets and to manipulate whole droplets. We address the advantages and disadvantages of the different techniques to guide new users.

Multichannel Dynamic Interfacial Printing: An Alternative Multicomponent Droplet Generation Technique for Lab in a Drop

Generation of uniform emulsion droplets mixed with multiple components is one of the key issues in the field of lab in a drop. Traditionally, droplet microfluidic chips are often served as the prime choice while designing and fabricating microfluidic chips always rely on skilled technician and specialized equipment, severely restricting its wide accessibility. In this work, an alternative technique, called multichannel dynamic interfacial printing (MC-DIP), was proposed for multicomponent droplet generation. The MC-DIP device was designed modularly and could be set up manually without any microfabrication process, exhibiting full accessibility for freshmen after a brief training. This new technique owns advantages in the generation of droplets with predictable sizes and composites. Quantitative experiments of measuring minimum inhibitory concentration (MIC) value via mixing microbes and antibiotics into droplet were conducted to proving its application potential for lab in a drop. Further research on a clinical pathogenic strain revealed that this technique could be potentially applied in the clinical laboratory for antibiotic susceptibility testing.

Sequential Coalescence Enabled Two-Step Microreactions in Triple-Core Double-Emulsion Droplets Triggered by an Electric Field

Advances in microfluidic emulsification have enabled the generation of exquisite multiple-core droplets, which are promising structures to accommodate microreactions. An essential requirement for conducting reactions is the sequential coalescence of the multiple cores encapsulated within these droplets, therefore, mixing the reagents together in a controlled sequence. Here, a microfluidic approach is reported for the conduction of two-step microreactions by electrically fusing three cores inside double-emulsion droplets. Using a microcapillary glass device, monodisperse water-in-oil-in-water droplets are fabricated with three compartmented reagents encapsulated inside. An AC electric field is then applied through a polydimethylsiloxane chip to trigger the sequential mixing of the reagents, where the precise sequence is guaranteed by the discrepancy of the volume or conductivity of the inner cores. A two-step reaction in each droplet is ensured by two times of core coalescence, which totally takes 20-40 s depending on varying conditions. The optimal parameters of the AC signal for the sequential fusion of the inner droplets are identified. Moreover, the capability of this technique is demonstrated by conducting an enzyme-catalyzed reaction used for glucose detection with the double-emulsion droplets. This technique should benefit a wide range of applications that require multistep reactions in micrometer scale.

In-droplet microparticle separation using travelling surface acoustic wave

Droplets in microfluidic systems can contain microscale objects such as cells and microparticles. The control of the positions of microscale objects within a microchannel is crucial for practical applications in not only continuous-flow-based but also droplet-based systems. This paper proposes an active method for the separation of microparticles inside moving droplets which uses travelling surface acoustic waves (TSAWs). We demonstrate the preconcentration and separation of 5 and 10 μm polystyrene microparticles in moving water-in-oil droplets through the application of TSAWs with two different frequencies. The microparticles inside the droplets are affected by the acoustic radiation force induced by the TSAWs to move laterally in the direction of the TSAW propagation and are thereby separated according to their size. In-droplet separation is then demonstrated through droplet splitting at a Y-junction. Compared to our previous studies, this acoustic approach offers the label-free and on-demand separation of different-sized micro-objects in moving droplets. The present method has potential uses such as in-droplet sample purification and enrichment.

Magnetic Janus particles synthesized using droplet micro-magnetofluidic techniques for protein detection

Magnetic droplets on a microfluidic platform can act as micro-robots, providing wireless, remote, and programmable control. This field of droplet micro-magnetofluidics (DMMF) is useful for droplet merging, mixing and synthesis of Janus structures. Specifically, magnetic Janus particles (MJP) are useful for protein and DNA detection as well as magnetically controlled bioprinting. However, synthesis of MJP with control of the functional phases is a challenge. Hence, we developed a high flow rate, surfactant-free, wash-less method to synthesize MJP by integration of DMMF with hybrid magnetic fields. The effects of the flow rate, flow rate ratio, and hybrid magnetic field on the magnetic component of the Janus droplets and the MJP were investigated. It was found that the magnetization, particle size, and phase distribution inside MJP could be readily tuned by the flow rates and the magnetic field. The magnetic component in the MJP could be concentrated after mixing at flow rate ratio values less than 7.5 and flow rates less than 3 ml h^-1. The experimental results and our simulations are in good agreement. The synthesized magnetic-fluorescent Janus particles were used for protein detection, with BSA as a model protein.

Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

Commercial Value and Challenges of Drop-Based Microfluidic Screening Platforms–An Opinion

Developments in High Throughput Screening aim at maximizing the number of samples per time and reducing the cost per sample, e.g., by applying very small sample volumes. The ultimate technological step in miniaturization is moving from microtiter plate wells to droplets, and from batch-wise characterization to the continuous preparation and analysis of samples. A range of drop-based microfluidic screening platforms has emerged that benefit from drop-formation rates of thousands per second, perfect drop size uniformity, plug-flow and compartmentalization, and the possibility of continuously analyzing a train of drops. However, after many years of intensive research, only few commercial applications have been developed and substantial development in the field is still required to make them reliable and broadly applicable. Can academic research achieve this, given that most of the fundamental concepts have been described already, making it hard to publish a big story? Can start-up companies raise enough money to overcome the technical issues of drop-based screening platforms? This contribution addresses the question, focusing on how the different stakeholders in the field should interact so that disillusionment will not put a premature end to the development of drop-based screening technologies.

Optimized droplet digital CFU assay (ddCFU) provides precise quantification of bacteria over a dynamic range of 6 logs and beyond

Standard digital assays need a large number of compartments for precise quantification of a sample over a broad dynamic range. We address this issue with an optimized droplet digital approach that uses a drastically reduced number of compartments for quantification. We generate serial logarithmic dilutions of an initial bacterial sample as an array of microliter-sized droplet plugs. In a subsequent step, these droplets are split into libraries of nanoliter droplets and pooled together for incubation and analysis. We show that our technology is at par with traditional dilution plate count for quantification of bacteria, but has the advantage of simplifying the experimental setup and reducing the manual workload. The method also has the potential to reduce the assay time significantly.

Review: Microbial analysis in dielectrophoretic microfluidic systems

Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques.

Stochastically reduced communities-Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces

Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet-based micro-segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets. Microfluidics was applied for the investigation and comparison of soil samples from ancient mining areas by highly resolved concentration-dependent screenings. As results, the generation, incubation, and in situ optical characterization of nanoliter droplets of suspensions of unknown soil microbial communities allowed the identification of different response characteristics toward heavy metal exposition. The investigations proved the high potential of microfluidics for investigations of soil microbial communities. It may be in the future helpful to detect bacteria and consortia with special biosorption characteristics, which could be useful for the development of biological accumulation and detoxification strategies.

K-Channel: A Multifunctional Architecture for Dynamically Reconfigurable Sample Processing in Droplet Microfluidics

By rapidly creating libraries of thousands of unique, miniaturized reactors, droplet microfluidics provides a powerful method for automating high-throughput chemical analysis. In order to engineer in-droplet assays, microfluidic devices must add reagents into droplets, remove fluid from droplets, and perform other necessary operations, each typically provided by a unique, specialized geometry. Unfortunately, modifying device performance or changing operations usually requires re-engineering the device among these specialized geometries, a time-consuming and costly process when optimizing in-droplet assays. To address this challenge in implementing droplet chemistry, we have developed the "K-channel," which couples a cross-channel flow to the segmented droplet flow to enable a range of operations on passing droplets. K-channels perform reagent injection (0-100% of droplet volume), fluid extraction (0-50% of droplet volume), and droplet splitting (1:1-1:5 daughter droplet ratio). Instead of modifying device dimensions or channel configuration, adjusting external conditions, such as applied pressure and electric field, selects the K-channel process and tunes its magnitude. Finally, interfacing a device-embedded magnet allows selective capture of 96% of droplet-encapsulated superparamagnetic beads during 1:1 droplet splitting events at ∼400 Hz. Addition of a second K-channel for injection (after the droplet splitting K-channel) enables integrated washing of magnetic beads within rapidly moving droplets. Ultimately, the K-channel provides an exciting opportunity to perform many useful droplet operations across a range of magnitudes without requiring architectural modifications. Therefore, we envision the K-channel as a versatile, easy to use microfluidic component enabling diverse, in-droplet (bio)chemical manipulations.

High-throughput system-wide engineering and screening for microbial biotechnology

Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes. More specifically, we will emphasize the use of multiplex automated genome evolution (MAGE) and CRISPR/Cas systems for high-throughput genome engineering and the application of (lab-on-chip) nanoreactors for high-throughput single-cell or population screening.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches.

Separation of main and satellite droplets in a deterministic lateral displacement microfluidic device

We present a novel DLD microfluidic device for preparing satellite-free main droplets and monodispersed satellite droplets.

Synthetic Protein Switches: Theoretical and Experimental Considerations

Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.

Morphology design and control of polymer particles by regulating the droplet flowing mode in microfluidic chips

Polymer particles with different morphologies were prepared by regulating the flowing mode of droplets.

Microfluidics cell sample preparation for analysis: Advances in efficient cell enrichment and precise single cell capture

Single cell analysis has received increasing attention recently in both academia and clinics, and there is an urgent need for effective upstream cell sample preparation. Two extremely challenging tasks in cell sample preparation-high-efficiency cell enrichment and precise single cell capture-have now entered into an era full of exciting technological advances, which are mostly enabled by microfluidics. In this review, we summarize the category of technologies that provide new solutions and creative insights into the two tasks of cell manipulation, with a focus on the latest development in the recent five years by highlighting the representative works. By doing so, we aim both to outline the framework and to showcase example applications of each task. In most cases for cell enrichment, we take circulating tumor cells (CTCs) as the target cells because of their research and clinical importance in cancer. For single cell capture, we review related technologies for many kinds of target cells because the technologies are supposed to be more universal to all cells rather than CTCs. Most of the mentioned technologies can be used for both cell enrichment and precise single cell capture. Each technology has its own advantages and specific challenges, which provide opportunities for researchers in their own area. Overall, these technologies have shown great promise and now evolve into real clinical applications.

Universal microfluidic platform for bioassays in anchored droplets

In spite of the large number of droplet-based microfluidic tools that have appeared in recent years, their penetration into non-specialist labs remains limited to a small number of applications. This is partly due to the lack of a generic platform that integrates all of the necessary operations for end-users, and partly to the increasing complexity that emerges as several operations are combined together. Here we report the development of a platform that provides the capabilities of multiwell plates in a two-dimensional array of nanoliter droplets: encapsulation, time-resolved monitoring and variation of well contents, as well as the ability to selectively extract the contents of any of the wells. We demonstrate these capabilities by encapsulating thousands of individual bacterial cells in droplets that are stored on a two-dimensional array of surface-energy anchors. Bacterial culture can be performed either in liquid or hydrogel droplets, both of which allow precise quantification using either standard measurements or digital enumeration. Using hydrogels allows the removal of the external oil that surrounds the aqueous drops, for instance in order to apply a gradient of antibiotics across the droplet population. This defines a protocol to obtain an antibiogram in a single experiment. Finally, the liquid to gel transition provides a robust way to selectively extract any droplet from the array, by melting it with a focused laser. When combined with further off-chip culture or genotyping, this platform provides a unique culturing environment to relate phenotype and genotype measurements on monoclonal colonies.

Emergence of microfluidic wearable technologies

There has been an intense interest in the development of wearable technologies, arising from increasing demands in the areas of fitness and healthcare. While still at an early stage, incorporating microfluidics in wearable technologies has enormous potential, especially in healthcare applications. For example, current microfluidic fabrication techniques can be innovatively modified to fabricate microstructures and incorporate electrically conductive elements on soft, flexible and stretchable materials. In fact, by leverarging on such microfabrication and liquid manipulation techniques, the developed flexible microfluidic wearable technologies have enabled several biosensing applications, including in situ sweat metabolites analysis, vital signs monitoring, and gait analysis. As such, we anticipate further significant breakthroughs and potential uses of wearable microfluidics in active drug delivery patches, soft robotics sensing and control, and even implantable artificial organs in the near future.