Effect of body shape on the motile behavior of bacteria-powered swimming microrobots (BacteriaBots)

MotGen: a closed-loop bacterial motility control framework using generative adversarial networks

MOTIVATION

Many organisms' survival and behavior hinge on their responses to environmental signals. While research on bacteria-directed therapeutic agents has increased, systematic exploration of real-time modulation of bacterial motility remains limited. Current studies often focus on permanent motility changes through genetic alterations, restricting the ability to modulate bacterial motility dynamically on a large scale. To address this gap, we propose a novel real-time control framework for systematically modulating bacterial motility dynamics.

RESULTS

We introduce MotGen, a deep learning approach leveraging Generative Adversarial Networks to analyze swimming performance statistics of motile bacteria based on live cell imaging data. By tracking objects and optimizing cell trajectory mapping under environmentally altered conditions, we trained MotGen on a comprehensive statistical dataset derived from real image data. Our experimental results demonstrate MotGen's ability to capture motility dynamics from real bacterial populations with low mean absolute error in both simulated and real datasets. MotGen allows us to approach optimal swimming conditions for desired motility statistics in real-time. MotGen's potential extends to practical biomedical applications, including immune response prediction, by providing imputation of bacterial motility patterns based on external environmental conditions. Our short-term, in-situ interventions for controlling motility behavior offer a promising foundation for the development of bacteria-based biomedical applications.

AVAILABILITY AND IMPLEMENTATION

MotGen is presented as a combination of Matlab image analysis code and a machine learning workflow in Python. Codes are available at https://github.com/bgmseo/MotGen, for cell tracking and implementation of trained models to generate bacterial motility statistics.

Chemical Approaches for the Preparation of Bacteria - Nano/Microparticle Hybrid Systems

Bacteria represent a class of living cells that are very attractive carriers for the transport and delivery of nano- and microsized particles. The use of cell-based carriers, such as for example bacteria, may allow to precisely direct nano- or microsized cargo to a desired site, which would greatly enhance the selectivity of drug delivery and allow to mitigate side effects. One key step towards the use of such nano-/microparticle - bacteria hybrids is the immobilization of the cargo on the bacterial cell surface. To fabricate bacteria - nano-/microparticle biohybrid microsystems, a wide range of chemical approaches are available that can be used to immobilize the particle payload on the bacterial cell surface. This article presents an overview of the various covalent and noncovalent chemistries that are available for the preparation of bacteria - nano-/microparticle hybrids. For each of the different chemical approaches, an overview will be presented that lists the bacterial strains that have been modified, the type and size of nanoparticles that have been immobilized, as well as the methods that have been used to characterize the nanoparticle-modified bacteria.

Biohybrid robots: recent progress, challenges, and perspectives

The past ten years have seen the rapid expansion of the field of biohybrid robotics. By combining engineered, synthetic components with living biological materials, new robotics solutions have been developed that harness the adaptability of living muscles, the sensitivity of living sensory cells, and even the computational abilities of living neurons. Biohybrid robotics has taken the popular and scientific media by storm with advances in the field, moving biohybrid robotics out of science fiction and into real science and engineering. So how did we get here, and where should the field of biohybrid robotics go next? In this perspective, we first provide the historical context of crucial subareas of biohybrid robotics by reviewing the past 10+ years of advances in microorganism-bots and sperm-bots, cyborgs, and tissue-based robots. We then present critical challenges facing the field and provide our perspectives on the vital future steps toward creating autonomous living machines.

Data-driven statistical modeling of the emergent behavior of biohybrid microrobots

Multi-agent biohybrid microrobotic systems, owing to their small size and distributed nature, offer powerful solutions to challenges in biomedicine, bioremediation, and biosensing. Synthetic biology enables programmed emergent behaviors in the biotic component of biohybrid machines, expounding vast potential benefits for building biohybrid swarms with sophisticated control schemes. The design of synthetic genetic circuits tailored toward specific performance characteristics is an iterative process that relies on experimental characterization of spatially homogeneous engineered cell suspensions. However, biohybrid systems often distribute heterogeneously in complex environments, which will alter circuit performance. Thus, there is a critically unmet need for simple predictive models that describe emergent behaviors of biohybrid systems to inform synthetic gene circuit design. Here, we report a data-driven statistical model for computationally efficient recapitulation of the motility dynamics of two types of Escherichia coli bacteria-based biohybrid swarms-NanoBEADS and BacteriaBots. The statistical model was coupled with a computational model of cooperative gene expression, known as quorum sensing (QS). We determined differences in timescales for programmed emergent behavior in BacteriaBots and NanoBEADS swarms, using bacteria as a comparative baseline. We show that agent localization and genetic circuit sensitivity strongly influence the timeframe and the robustness of the emergent behavior in both systems. Finally, we use our model to design a QS-based decentralized control scheme wherein agents make independent decisions based on their interaction with other agents and the local environment. We show that synergistic integration of synthetic biology and predictive modeling is requisite for the efficient development of biohybrid systems with robust emergent behaviors.

Rotating oil droplets driven by motile bacteria at interfaces

We show that oil droplets suspended near a liquid-solid interface can be driven to rotate by motile bacteria adhered to the droplet surface. Droplets rotate clockwise when viewed from the liquid side, due to symmetry-breaking hydrodynamic interactions of bacteria with the interface. The angular speed of rotation for droplets decreases as their size is increased. Differences in the speed of rotation driven by Escherichia coli, Shewanella haliotis, and Halomonas titanicae bacteria reflects differences in the number of bacteria adhered at the droplet surface and their interfacial affinity. Adding surfactant reduces the number of adherent bacteria and hence lowers the speed of rotation. Together, these results demonstrate that bacterial activity can be used to manipulate suspended droplets.

A hydrodynamic-stochastic model of chemotactic ciliated microorganisms

Biological systems like ciliated microorganisms are capable of responding to the external chemical gradients, a process known as chemotaxis. In this process, the internal signaling network of the microorganism is triggered due to binding of the chemoattractant molecules with the receptors on the surface of the body. This can alter the activity at the surface of the microorganism. We study the chemotaxis of ciliated microorganisms using the chiral squirmer model, a spherical body with a surface slip velocity. In the presence of a chemical gradient, the coefficients of the slip velocity get modified resulting in a change in the path followed by the body. We observe that the strength of the gradient is not the only parameter which controls the dynamics of the body but also the adaptation time plays a very significant role in the success of chemotaxis. The trajectory of the body is smooth if we ignore the discreteness in the ligand-receptor binding which is stochastic in nature. In the presence of the latter, the path is not only irregular but the whole dynamics of the body changes. We calculate the mean first passage time, by varying the strength of the chemical gradient and the adaptation time, to determine the success rate of chemotaxis.

Bacterial Biohybrid Microswimmers

Over millions of years, Nature has optimized the motion of biological systems at the micro and nanoscales. Motor proteins to motile single cells have managed to overcome Brownian motion and solve several challenges that arise at low Reynolds numbers. In this review, we will briefly describe naturally motile systems and their strategies to move, starting with a general introduction that surveys a broad range of developments, followed by an overview about the physical laws and parameters that govern and limit motion at the microscale. We characterize some of the classes of biological microswimmers that have arisen in the course of evolution, as well as the hybrid structures that have been constructed based on these, ranging from Montemagno's ATPase motor to the SpermBot. Thereafter, we maintain our focus on bacteria and their biohybrids. We introduce the inherent properties of bacteria as a natural microswimmer and explain the different principles bacteria use for their motion. We then elucidate different strategies that have been employed for the coupling of a variety of artificial microobjects to the bacterial surface, and evaluate the different effects the coupled objects have on the motion of the "biohybrid." Concluding, we give a short overview and a realistic evaluation of proposed applications in the field.

Cargo carrying bacteria at interfaces

The displacements of ensembles of colloids at the interface between oil and suspensions of the bacterium Pseudomonas aeruginosa PA14ΔpelA indicate enhanced colloid mobilities and apparently diffusive motion driven by interactions with the bacteria. However, inspection of individual trajectories of ∼500 particles reveals prolonged, directed displacements inconsistent with purely hydrodynamic interactions between swimming bacteria and colloids. Analysis of the properties of colloid paths indicates trajectories can be sorted into four distinct categories, including diffusive, persistent, curly, and mixed trajectory types. Non-diffusive trajectories are the norm, comprising 2/3 of the observed trajectories. Imaging of colloids in the interface reveals anisotropic assemblies formed by colloids decorated with one or more adhered bacteria that drive the colloids along these paths. The trajectories and enhanced transport result from individual colloids being moved as cargo by these adhered bacteria. The implications of these structures and open questions for interfacial transport are discussed and related to the active colloid literature.

Artificial Magnetotaxis of Microbot: Magnetophoresis versus Self-Swimming

An artificial magnetotactic microbot was created by integrating the microalgal cell with magnetic microbead for its potential application as biomotor in microscale environment. Here, we demonstrate the remote magnetotactic control of the microbot under a low gradient magnetic field (<100 T/m). We characterize the kinematic behavior of the microbots carrying magnetic microbeads of two different sizes, with diameter of 2 and 4.5 μm, in the absence and presence of magnetic field. In the absence of magnetic field, we observed the microbot showed a helical motion as a result of the misalignment between the thrust force and the symmetry axis after the attachment. The microbot bound with a larger magnetic microbead moved with higher translational velocity but rotated slower about its axis of rotation. The viscous force was balanced by the thrust force of the microbot, resulting in a randomized swimming behavior of the microbot at its terminal velocity. Meanwhile, under the influence of a low gradient magnetic field, we demonstrated that the directional control of the microbot was based on following principles: (1) magnetophoretic force was insignificant on influencing its perpendicular motion and (2) its parallel motion was dependent on both self-swimming and magnetophoresis, in which this cooperative effect was a function of separation distance from the magnet. As the microbot approached the magnet, the magnetophoretic force suppressed its self-swimming behavior, leading to a positive magnetotaxis of the microbot toward the source of magnetic field. Our experimental results and kinematic analysis revealed the contribution of mass density variation of particle-and-cell system on influencing its dynamical behavior.

Motility and chemotaxis of bacteria-driven microswimmers fabricated using antigen 43-mediated biotin display

Bacteria-driven biohybrid microswimmers (bacteriabots) combine synthetic cargo with motile living bacteria that enable propulsion and steering. Although fabrication and potential use of such bacteriabots have attracted much attention, existing methods of fabrication require an extensive sample preparation that can drastically decrease the viability and motility of bacteria. Moreover, chemotactic behavior of bacteriabots in a liquid medium with chemical gradients has remained largely unclear. To overcome these shortcomings, we designed Escherichia coli to autonomously display biotin on its cell surface via the engineered autotransporter antigen 43 and thus to bind streptavidin-coated cargo. We show that the cargo attachment to these bacteria is greatly enhanced by motility and occurs predominantly at the cell poles, which is greatly beneficial for the fabrication of motile bacteriabots. We further performed a systemic study to understand and optimize the ability of these bacteriabots to follow chemical gradients. We demonstrate that the chemotaxis of bacteriabots is primarily limited by the cargo-dependent reduction of swimming speed and show that the fabrication of bacteriabots using elongated E. coli cells can be used to overcome this limitation.

Construction of Bacteria-Based Cargo Carriers for Targeted Cancer Therapy

Despite significant recent progress in nanomedicine, drug delivery to solid tumors remains a formidable challenge often associated with low delivery efficiency and limited penetration of the drug in poorly vascularized regions of solid tumors. Attenuated strains of facultative anaerobes have been demonstrated to have exceptionally high selectivity to primary tumors and metastatic cancer, a good safety profile, and superior intratumoral penetration performance. However, bacteria have rarely been able to completely inhibit tumor growth in immunocompetent hosts solely by their presence in the tumor. We have developed a Nanoscale Bacteria-Enabled Autonomous Drug Delivery System (NanoBEADS) in which the functional capabilities of tumor-targeting bacteria are interfaced with chemotherapeutic-loaded nanoparticles, an approach that would amplify the therapeutic potential of both modalities. Here, we describe two biomanufacturing techniques to construct NanoBEADS by linking different bacterial species with polymeric theranostic vehicles. NanoBEADS are envisioned to significantly impact current practices in cancer theranostics through improved targeting and intratumoral transport properties.

Multifunctional Bacteria-Driven Microswimmers for Targeted Active Drug Delivery

High-performance, multifunctional bacteria-driven microswimmers are introduced using an optimized design and fabrication method for targeted drug delivery applications. These microswimmers are made of mostly single Escherichia coli bacterium attached to the surface of drug-loaded polyelectrolyte multilayer (PEM) microparticles with embedded magnetic nanoparticles. The PEM drug carriers are 1 μm in diameter and are intentionally fabricated with a more viscoelastic material than the particles previously studied in the literature. The resulting stochastic microswimmers are able to swim at mean speeds of up to 22.5 μm/s. They can be guided and targeted to specific cells, because they exhibit biased and directional motion under a chemoattractant gradient and a magnetic field, respectively. Moreover, we demonstrate the microswimmers delivering doxorubicin anticancer drug molecules, encapsulated in the polyelectrolyte multilayers, to 4T1 breast cancer cells under magnetic guidance in vitro. The results reveal the feasibility of using these active multifunctional bacteria-driven microswimmers to perform targeted drug delivery with significantly enhanced drug transfer, when compared with the passive PEM microparticles.

Bioadhesive Bacterial Microswimmers for Targeted Drug Delivery in the Urinary and Gastrointestinal Tracts

Bacteria-driven biohybrid microswimmers (bacteriabots), which integrate motile bacterial cells and functional synthetic cargo parts (e.g., microparticles encapsulating drug), are recently studied for targeted drug delivery. However, adhesion of such bacteriabots to the tissues on the site of a disease (which can increase the drug delivery efficiency) is not studied yet. Here, this paper proposes an approach to attach bacteriabots to certain types of epithelial cells (expressing mannose on the membrane), based on the affinity between lectin molecules on the tip of bacterial type I pili and mannose molecules on the epithelial cells. It is shown that the bacteria can anchor their cargo particles to mannose-functionalized surfaces and mannose-expressing cells (ATCC HTB-9) using the lectin-mannose bond. The attachment mechanism is confirmed by comparing the adhesion of bacteriabots fabricated from bacterial strains with or without type I pili to mannose-covered surfaces and cells. The proposed bioadhesive motile system can be further improved by expressing more specific adhesion moieties on the membrane of the bacteria.

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria

Bacteria biohybrids employ the motility and power of swimming bacteria to carry and maneuver microscale particles. They have the potential to perform microdrug and cargo delivery in vivo, but have been limited by poor design, reduced swimming capabilities, and impeded functionality. To address these challenge, motile Escherichia coli are captured inside electropolymerized microtubes, exhibiting the first report of a bacteria microswimmer that does not utilize a spherical particle chassis. Single bacterium becomes partially trapped within the tube and becomes a bioengine to push the microtube though biological media. Microtubes are modified with "smart" material properties for motion control, including a bacteria-attractant polydopamine inner layer, addition of magnetic components for external guidance, and a biochemical kill trigger to cease bacterium swimming on demand. Swimming dynamics of the bacteria biohybrid are quantified by comparing "length of protrusion" of bacteria from the microtubes with respect to changes in angular autocorrelation and swimmer mean squared displacement. The multifunctional microtubular swimmers present a new generation of biocompatible micromotors toward future microbiorobots and minimally invasive medical applications.

Bioengineered and biohybrid bacteria-based systems for drug delivery

The use of bacterial cells as agents of medical therapy has a long history. Research that was ignited over a century ago with the accidental infection of cancer patients has matured into a platform technology that offers the promise of opening up new potential frontiers in medical treatment. Bacterial cells exhibit unique characteristics that make them well-suited as smart drug delivery agents. Our ability to genetically manipulate the molecular machinery of these cells enables the customization of their therapeutic action as well as its precise tuning and spatio-temporal control, allowing for the design of unique, complex therapeutic functions, unmatched by current drug delivery systems. Early results have been promising, but there are still many important challenges that must be addressed. We present a review of promises and challenges of employing bioengineered bacteria in drug delivery systems and introduce the biohybrid design concept as a new additional paradigm in bacteria-based drug delivery.

Optical assembly of bio-hybrid micro-robots

The combination of micro synthetic structures with bacterial flagella motors represents an actual trend for the construction of self-propelled micro-robots. The development of methods for fabrication of these bacteria-based robots is a first crucial step towards the realization of functional miniature and autonomous moving robots. We present a novel scheme based on optical trapping to fabricate living micro-robots. By using holographic optical tweezers that allow three-dimensional manipulation in real time, we are able to arrange the building blocks that constitute the micro-robot in a defined way. We demonstrate exemplarily that our method enables the controlled assembly of living micro-robots consisting of a rod-shaped prokaryotic bacterium and a single elongated zeolite L crystal, which are used as model of the biological and abiotic components, respectively. We present different proof-of-principle approaches for the site-selective attachment of the bacteria on the particle surface. The propulsion of the optically assembled micro-robot demonstrates the potential of the proposed method as a powerful strategy for the fabrication of bio-hybrid micro-robots.

Modeling of chemotactic steering of bacteria-based microrobot using a population-scale approach

The bacteria-based microrobot (Bacteriobot) is one of the most effective vehicles for drug delivery systems. The bacteriobot consists of a microbead containing therapeutic drugs and bacteria as a sensor and an actuator that can target and guide the bacteriobot to its destination. Many researchers are developing bacteria-based microrobots and establishing the model. In spite of these efforts, a motility model for bacteriobots steered by chemotaxis remains elusive. Because bacterial movement is random and should be described using a stochastic model, bacterial response to the chemo-attractant is difficult to anticipate. In this research, we used a population-scale approach to overcome the main obstacle to the stochastic motion of single bacterium. Also known as Keller-Segel's equation in chemotaxis research, the population-scale approach is not new. It is a well-designed model derived from transport theory and adaptable to any chemotaxis experiment. In addition, we have considered the self-propelled Brownian motion of the bacteriobot in order to represent its stochastic properties. From this perspective, we have proposed a new numerical modelling method combining chemotaxis and Brownian motion to create a bacteriobot model steered by chemotaxis. To obtain modeling parameters, we executed motility analyses of microbeads and bacteriobots without chemotactic steering as well as chemotactic steering analysis of the bacteriobots. The resulting proposed model shows sound agreement with experimental data with a confidence level <0.01.

Directed transport of bacteria-based drug delivery vehicles: bacterial chemotaxis dominates particle shape

Several attenuated and non-pathogenic bacterial species have been demonstrated to actively target diseased sites and successfully deliver plasmid DNA, proteins and other therapeutic agents into mammalian cells. These disease-targeting bacteria can be employed for targeted delivery of therapeutic and imaging cargos in the form of a bio-hybrid system. The bio-hybrid drug delivery system constructed here is comprised of motile Escherichia coli MG1655 bacteria and elliptical disk-shaped polymeric microparticles. The transport direction for these vehicles can be controlled through biased random walk of the attached bacteria in presence of chemoattractant gradients in a process known as chemotaxis. In this work, we utilize a diffusion-based microfluidic platform to establish steady linear concentration gradients of a chemoattractant and investigate the roles of chemotaxis and geometry in transport of bio-hybrid drug delivery vehicles. Our experimental results demonstrate for the first time that bacterial chemotactic response dominates the effect of body shape in extravascular transport; thus, the non-spherical system could be more favorable for drug delivery applications owing to the known benefits of using non-spherical particles for vascular transport (e.g. relatively long circulation time).

Bio-hybrid cell-based actuators for microsystems

As we move towards the miniaturization of devices to perform tasks at the nano and microscale, it has become increasingly important to develop new methods for actuation, sensing, and control. Over the past decade, bio-hybrid methods have been investigated as a promising new approach to overcome the challenges of scaling down robotic and other functional devices. These methods integrate biological cells with artificial components and therefore, can take advantage of the intrinsic actuation and sensing functionalities of biological cells. Here, the recent advancements in bio-hybrid actuation are reviewed, and the challenges associated with the design, fabrication, and control of bio-hybrid microsystems are discussed. As a case study, focus is put on the development of bacteria-driven microswimmers, which has been investigated as a targeted drug delivery carrier. Finally, a future outlook for the development of these systems is provided. The continued integration of biological and artificial components is envisioned to enable the performance of tasks at a smaller and smaller scale in the future, leading to the parallel and distributed operation of functional systems at the microscale.

Velocity Fluctuations in Helical Propulsion: How Small Can a Propeller Be

Helical propulsion is at the heart of locomotion strategies utilized by various natural and artificial swimmers. We used experimental observations and a numerical model to study the various fluctuation mechanisms that determine the performance of an externally driven helical propeller as the size of the helix is reduced. From causality analysis, an overwhelming effect of orientational noise at low length scales is observed, which strongly affects the average velocity and direction of motion of a propeller. For length scales smaller than a few micrometers in aqueous media, the operational frequency for the propulsion system would have to increase as the inverse cube of the size, which can be the limiting factor for a helical propeller to achieve locomotion in the desired direction.