Dissolvable alginate hydrogel-based biofilm microreactors for antibiotic susceptibility assays

Biofilms are found in many infections in the forms of surface-adhering aggregates on medical devices, small clumps in tissues, or even in synovial fluid. Although antibiotic resistance genes are studied and monitored in the clinic, the structural and phenotypic changes that take place in biofilms can also lead to significant changes in how bacteria respond to antibiotics. Therefore, it is important to better understand the relationship between biofilm phenotypes and resistance and develop approaches that are compatible with clinical testing. Current methods for studying antimicrobial susceptibility are mostly planktonic or planar biofilm reactors. In this work, we develop a new type of biofilm reactor-three-dimensional (3D) microreactors-to recreate biofilms in a microenvironment that better mimics those in vivo where bacteria tend to form surface-independent biofilms in living tissues. The microreactors are formed on microplates, treated with antibiotics of 1000 times of the corresponding minimal inhibitory concentrations (1000 × MIC), and monitored spectroscopically with a microplate reader in a high-throughput manner. The hydrogels are dissolvable on demand without the need for manual scraping, thus enabling measurements of phenotypic changes. Bacteria inside the biofilm microreactors are found to survive exposure to 1000 × MIC of antibiotics, and subsequent comparison with plating results reveals no antibiotic resistance-associated phenotypes. The presented microreactor offers an attractive platform to study the tolerance and antibiotic resistance of surface-independent biofilms such as those found in tissues.

Programmable Physical Properties of Freestanding Chitosan Membranes Electrofabricated in Microfluidics

Microfluidic-integrated freestanding membranes with suitable biocompatibility and tunable physicochemical properties are in high demand for a wide range of life science and biological studies. However, there is a lack of facile and rapid methods to integrate such versatile membranes into microfluidics. A recently invented interfacial electrofabrication of chitosan membranes offers an in-situ membrane integration strategy that is flexible, controllable, simple, and biologically friendly. In this follow-up study, we explored the ability to program the physical properties of these chitosan membranes by varying the electrofabrication conditions (e.g., applied voltage and pH of alginate). We found a strong association between membrane growth rate, properties, and fabrication parameters: high electrical stimuli and pH of alginate resulted in high optical retardance and low permeability, and vice versa. This suggests that the molecular alignment and density of electrofabricated chitosan membranes could be actively tailored according to application needs. Lastly, we demonstrated that this interfacial electrofabrication could easily be expanded to produce chitosan membrane arrays with higher uniformity than the previously well-established flow assembly method. This study demonstrates the tunability of the electrofabricated membranes' properties and functionality, thus expanding the utility of such membranes for broader applications in the future.

Probing mutual interactions between Pseudomonas aeruginosa and Candida albicans in a biofabricated membrane-based microfluidic platform

Microbes are typically found in multi-species (polymicrobial) communities. Cooperative and competitive interactions between species, mediated by diffusible factors and physical contact, leads to highly dynamic communities that undergo changes in composition diversity and size. Infections can be more severe or more difficult to treat when caused by multiple species. Interactions between species can improve the ability of one or more species to tolerate anti-microbial treatments and host defenses. Pseudomonas aeruginosa (Pa), a ubiquitous bacterium, and the opportunistic pathogenic yeast, Candida albicans (Ca), are frequently found together in cystic fibrosis lung infections and wound infections. While significant progress has been made in determining interactions between Pa and Ca, there are still important questions that remain unanswered. Here, we probe the mutual interactions between Pa and Ca in a custom-made microfluidic device using biopolymer chitosan membranes that support cross-species communication. By assembling microbes in physically separated, chemically communicating populations or bringing into direct interactions in a mixed culture, in situ polymicrobial growth and biofilm morphology were qualitatively characterized and quantified. Our work reveals new dynamic details of their mutual interactions including cooperation, competition, invasion, and biofilm formation. The membrane-based microfluidic platform can be further developed to understand the polymicrobial interactions within a controlled interactive microenvironment to improve microbial infection prevention and treatment.

Dual-modality digital holographic and polarization microscope to quantify phase and birefringence signals in biospecimens with a complex microstructure

Optical phase and birefringence signals occur in cells and thin, semi-transparent biomaterials. A dual-modality quantitative phase and polarization microscope was designed to study the interaction of cells with extracellular matrix networks and to relate optical pathlength and birefringence signals within structurally anisotropic biomaterial constructs. The design was based on an existing, custom-built digital holographic microscope, to which was added a polarization microscope utilizing liquid crystal variable retarders. Phase and birefringence channels were calibrated, and data was acquired sequentially from cell-seeded collagen hydrogels and electrofabricated chitosan membranes. Computed phase height and retardance from standard targets were accurate within 99.7% and 99.8%, respectively. Phase height and retardance channel background standard deviations were 35 nm and 0.6 nm, respectively. Human fibroblasts, visible in the phase channel, aligned with collagen network microstructure, with retardance and azimuth visible in the polarization channel. Electrofabricated chitosan membranes formed in 40 µm tall microfluidic channels possessed optical retardance ranging from 7 to 11 nm, and phase height from 37 to 39 µm. These results demonstrate co-registered dual-channel acquisition of phase and birefringence parameter maps from microstructurally-complex biospecimens using a novel imaging system combining digital holographic microscopy with voltage-controlled polarization microscopy.

Flow-assembled chitosan membranes in microfluidics: recent advances and applications

The integration of membranes in microfluidic devices has been extensively exploited for various chemical engineering and bioengineering applications over the past few decades. To augment the applicability of membrane-integrated microfluidic platforms for biomedical and tissue engineering studies, a biologically friendly fabrication process with naturally occurring materials is highly desired. The in situ preparation of membranes involving interfacial reactions between parallel laminar flows in microfluidic networks, known as the flow-assembly technique, is one of the most biocompatible approaches. Membranes of many types with flexible geometries have been successfully assembled inside complex microchannels using this facile and versatile flow-assembly approach. Chitosan is a naturally abundant polysaccharide known for its pronounced biocompatibility, biodegradability, good mechanical stability, ease of modification and processing, and film-forming ability under near-physiological conditions. Chitosan membranes assembled by flows in microfluidics are freestanding, robust, semipermeable, and well-aligned in microstructure, and show high affinity to bioactive reagents and biological components (e.g. biomolecules, nanoparticles, or cells) that provide facile biological functionalization of microdevices. Here, we discuss the recent developments and optimizations in the flow-assembly of chitosan membranes and chitosan-based membranes in microfluidics. Furthermore, we recapitulate the applications of the chitosan membrane-integrated microfluidic platforms dedicated to biology, biochemistry, and drug release fields, and envision the future developments of this important platform with versatile functions.

Microfluidic and mathematical modeling of aquatic microbial communities

Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.

Microfluidic fabrication of stable collagen microgels with aligned microstructure using flow-driven co-deposition and ionic gelation

The controlled biofabrication of stable, aligned collagen hydrogels within microfluidic devices is critically important to the design of more physiologically accurate, longer-cultured on-chip models of tissue and organs. To address this goal, collagen-alginate microgels were formed in a microfluidic channel by calcium crosslinking of a flowing collagen-alginate solution through a cross-channel chitosan membrane spanning a pore allowing ion diffusion but not convection. The gels formed within seconds as isolated islands in a single channel, and their growth was self-limiting. Total gel thickness was controlled by altering the concentration of calcium and collagen-alginate flow rate to reach an equilibrium of calcium diffusion and solution convection at the gel boundary, for a desired thickness of 30-200 μm. Additionally, less calcium and higher flow produced greater compression of the gel, with regions farther from the pore compressing more. An aligned, stable collagen network was demonstrated by collagen birefringence, circumferential texture orientation, and little change in gel dimensions with de-chelation of calcium from alginate by prolonged flow of EDTA in the channel. Resultant gels were most stable and only slightly asymmetric when formed from solutions containing 8 mg ml^-1 collagen. Diffusion of 4 kDa and 70 kDa fluorescently-labeled dextran indicated size-dependent diffusion across the gel, and accessibility of the construct to appropriately-sized bioactive molecules. This work demonstrates the physicochemical parameter control of collagen gel formation in microfluidic devices, with utility toward on-chip models of dense extracellular matrix invasion, cancer growth and drug delivery to cells within dense extracellular matrix bodies.

The engineering of spatially linked microbial consortia - potential and perspectives

Traditional biotechnological applications of microorganisms employ mono-cultivation or co-cultivation in well-mixed vessels disregarding the potential of spatially organized cultures. Metabolic specialization and guided species interactions facilitated through spatial isolation would enable consortia of microbes to accomplish more complex functions than currently possible, for bioproduction as well as biodegradation processes. Here, we review concepts of spatially linked microbial consortia in which spatial arrangement is optimized to increase control and facilitate new species combinations. We highlight that genome-scale metabolic network models can inform the design and tuning of synthetic microbial consortia and suggest that a standardized assembly of such systems allows the combination of 'incompatibles', potentially leading to countless novel applications.

Modulating the properties of flow-assembled chitosan membranes in microfluidics with glutaraldehyde crosslinking

Glutaraldehyde crosslinking significantly enhances the mechanical robustness of the originally compromised flow-assembled chitosan membranes after Pluronic passivation in microfluidics.

Chemotropism among populations of yeast cells with spatiotemporal resolution in a biofabricated microfluidic platform

Chemotropism is an essential response of organisms to external chemical gradients that direct the growth of cells toward the gradient source. Chemotropic responses between single cells have been studied using in vitro gradients of synthetically derived signaling molecules and helped to develop a better understanding of chemotropism in multiple organisms. However, dynamic changes including spatial changes to the gradient as well as fluctuations in levels of cell generated signaling molecules can result in the redirection of chemotropic responses, which can be difficult to model with synthetic peptides and single cells. An experimental system that brings together populations of cells to monitor the population-scale chemotropic responses yet retain single cell spatiotemporal resolution would be useful to further inform on models of chemotropism. Here, we describe a microfluidic platform that can measure the chemotropic response between populations of mating yeast A- and α-cells with spatiotemporal programmability and sensitivity by positioning cell populations side by side in calcium alginate hydrogels along semipermeable membranes with micrometer spatial control. The mating phenotypes of the yeast populations were clearly observed over hours. Three distinct responses were observed depending on the distance between the A- and α-cell populations: the cells either continued to divide, arrest, and develop a stereotypical polarized projection termed a "shmoo" toward the cells of opposite mating type or formed shmoos in random directions. The results from our studies of yeast mating suggest that the biofabricated microfluidic platform can be adopted to study population-scale, spatial-sensitive cell-cell signaling behaviors that would be challenging using conventional approaches.

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials

The human oral mucosa hosts a diverse microbiome and is exposed to potentially toxic biomaterials from dental restoratives. Mucosal health is partly determined by cell and tissue responses to challenges such as dental materials and pathogenic bacteria. An in vitro model to rapidly determine potential layer-specific responses would lead to a better understanding of mucosal homeostasis and pathology. Therefore, this study aimed to develop a co-cultured microfluidic mucosal model on-a-chip to rapidly assess mucosal remodeling and the responses of epithelial and subepithelial layers to challenges typically found in the oral environment. A gingival fibroblast-laden collagen hydrogel was assembled in the central channel of a three-channel microfluidic chamber with interconnecting pores, followed by a keratinocyte layer attached to the collagen exposed in the pores. This configuration produced apical and subepithelial side channels capable of sustaining flow. Keratinocyte, fibroblast, and collagen densities were optimized to create a co-culture tissue-like construct stable over one week. Cells were stained and imaged with epifluorescence microscopy to confirm layer characteristics. As proof-of-concept, the mucosal construct was exposed separately to a dental monomer, 2-hydroxylethyl methacrylate (HEMA), and the oral bacteria Streptococcus mutans. Exposure to HEMA lowered mucosal cell viability, while exposure to the bacteria lowered trans-epithelial electrical resistance. These findings suggest that the oral mucosa-on-a-chip is useful for studying oral mucosal interactions with bacteria and biomaterials with a histology-like view of the tissue layers.