Intra-species bacterial quorum sensing studied at single cell level in a double droplet trapping system

Quorum sensing communication between lipid-based artificial cells

Population behavior based on quorum sensing communication is a key property of living microorganisms. Here, we show quorum sensing behavior in an artificial cell population consisting of giant lipid vesicles loaded with sender-receiver machinery (enzymes and responsive biomolecules). Our system allows the examination of the collective output based on cell density, fuel concentration and proximity, which are important factors controlling natural quorum sensing behavior.

Tracking the stochastic growth of bacterial populations in microfluidic droplets

Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicate Escherichia coli populations within droplets. {We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.

Growing from a few cells: combined effects of initial stochasticity and cell-to-cell variability

The growth of a cell population from a large inoculum appears deterministic, although the division process is stochastic at the single-cell level. Microfluidic observations, however, display wide variations in the growth of small populations. Here we combine theory, simulations and experiments to explore the link between single-cell stochasticity and the growth of a population starting from a small number of individuals. The study yields descriptors of the probability distribution function (PDF) of the population size under three sources of stochasticity: cell-to-cell variability, uncertainty in the number of initial cells and generation-dependent division times. The PDF, rescaled to account for the exponential growth of the population, is found to converge to a stationary distribution. All moments of the PDF grow exponentially with the same growth rate, which depends solely on cell-to-cell variability. The shape of the PDF, however, contains the signature of all sources of stochasticity, and is dominated by the early stages of growth, and not by the cell-to-cell variability. Thus, probabilistic predictions of the growth of bacterial populations can be obtained with implications for both naturally occurring conditions and technological applications of single-cell microfluidics.

Microbial interactions trigger the production of antibiotics

Since the discovery of penicillin, antibiotics have been instrumental in treating infectious diseases. However, emerging antibiotic multi-resistance coinciding with a nearly exhausted drug pipeline is a major concern for the future of the therapy of infections. A novel approach for the discovery of antibiotics relies on the analysis of microbial consortia in their ecological context, taking into account the potential natural role of antibiotics. Co-cultivations of microorganisms have been successfully applied for the isolation of unknown secondary metabolites including antibiotics, and, thus, open new avenues to the production of bioactive compounds while at the same time providing insight into the natural function of the produced molecules and the regulation of their formation.

Beyond the bulk: disclosing the life of single microbial cells

Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community

The activity of a biological community is the outcome of complex processes involving interactions between community members. It is often unclear how to accurately incorporate these interactions into predictive models. Previous work has shown a range of positive and negative metabolic pairwise interactions between species. Here we examine the ability of a modified general Lotka-Volterra model with cell-cell interaction coefficients to predict the overall metabolic rate of a well-mixed microbial community comprised of four heterotrophic natural isolates, experimentally quantifying the strengths of two, three, and four-species interactions. Within this community, interactions between any pair of microbial species were positive, while higher-order interactions, between 3 or more microbial species, slightly modulated community metabolism. For this simple community, the metabolic rate of can be well predicted only with taking into account pairwise interactions. Simulations using the experimentally determined interaction parameters revealed that spatial heterogeneity in the distribution of cells increased the importance of multispecies interactions in dictating function at both the local and global scales.

Many wild microbial ecosystems contain hundreds to thousands of species, suggesting that interactions between species likely play an important role in regulating the behavior of such complex cellular networks. Predicting how these interactions impact the overall activity of microbial communities remains a challenge. Here we quantify the contribution of interactions between more than two species to the overall metabolic rate of a mixture of four freshwater bacteria. We systematically measure interactions between these species and use theoretical models to examine the influence cell-cell interactions on spatially non-uniform microbial populations. Our results demonstrate that although interactions between species are key regulators of system behavior, only considering interactions between pairs of species is sufficient to predict ecosystem activity. Simulations demonstrate that activity at both the single-cell and population level would be strongly influenced by how microbes are distributed in space. These findings improve our understanding of how best to examine groups of microbes that coexist in environments such as soil, water, and the human body.

Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis

This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.

Droplet microfluidics for microbiology: techniques, applications and challenges

Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.

Microfluidics and microbial engineering

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

Fluorescence-based tools for single-cell approaches in food microbiology

The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology.

Stationary nanoliter droplet array with a substrate of choice for single adherent/nonadherent cell incubation and analysis

Microfluidic water-in-oil droplets that serve as separate, chemically isolated compartments can be applied for single-cell analysis; however, to investigate encapsulated cells effectively over prolonged time periods, an array of droplets must remain stationary on a versatile substrate for optimal cell compatibility. We present here a platform of unique geometry and substrate versatility that generates a stationary nanodroplet array by using wells branching off a main microfluidic channel. These droplets are confined by multiple sides of a nanowell and are in direct contact with a biocompatible substrate of choice. The device is operated by a unique and reversed loading procedure that eliminates the need for fine pressure control or external tubing. Fluorocarbon oil isolates the droplets and provides soluble oxygen for the cells. By using this approach, the metabolic activity of single adherent cells was monitored continuously over time, and the concentration of viable pathogens in blood-derived samples was determined directly by measuring the number of colony-formed droplets. The method is simple to operate, requires a few microliters of reagent volume, is portable, is reusable, and allows for cell retrieval. This technology may be particularly useful for multiplexed assays for which prolonged and simultaneous visual inspection of many isolated single adherent or nonadherent cells is required.

Frontier microfluidic techniques for short and long-term single cell analysis

Here, we review the frontier microfluidic techniques for single cell analysis (SCA), which is important for research of many biological systems. Microfluidics provides high-throughput, high-resolution experiments at low cost and reagent use, making it especially useful for single cell analysis. Recent advancements in the field have made SCA more feasible, improving device throughput and resolution, adding capabilities, and combining different functions to bring forth new assays. Developments in incubation have allowed for long-term cell tracking assays to be performed with single cell resolution. The ability of systems to provide chemical isolation or prolonged growth of adherent cells is also discussed.

Communication and computation by bacteria compartmentalized within microemulsion droplets

Amphiphilic inducer molecules such as N-acyl-L-homoserine lactones (AHLs) or isopropyl-β-D-thio-galactopyranoside (IPTG) can be utilized for the implementation of an artificial communication system between groups of E. coli bacteria encapsulated within water-in-oil microemulsion droplets. Using spatially extended arrays of microdroplets, we study the diffusion of both AHL and IPTG from inducer-filled reservoirs into bacteria-containing droplets, and also from droplets with AHL producing sender bacteria into neighboring droplets containing receiver cells. Computational modeling of gene expression dynamics within the droplets suggests a strongly reduced effective diffusion coefficient of the inducers, which markedly affects the spatial communication pattern in the neighborhood of the senders. Engineered bacteria that integrate AHL and IPTG signals with a synthetic AND gate gene circuit are shown to respond only in the presence of both types of sender droplets, which demonstrates the potential of the system for genetically programmed pattern formation and distributed computing.