Dynamics of bacterial streamers induced clogging in microfluidic devices

The porous structure induced heterogeneous and localized failure of the biofilm in microfluidic channels

Understanding the mechanism of biofilm distribution and detachment is very important to effectively improve water treatment and prevent blockage in porous media. The existing research is more related to the local biofilm evolving around one or few microposts and the lack of the integral biofilm evolution in a micropost array for a longer growth period. This study combines microfluidic experiments and mathematical simulations to study the distribution and detachment of biofilm in porous media. Microfluidic chips with an array of microposts with different sizes are designed to simulate the physical pore structure of soil. The research shows that the initial formation and distribution of biofilm are influenced by bacterial transport velocity gradients within the pore space. Bacteria prefer to aggregate areas with smaller microposts, leading to the development of biofilm in those regions. Consequently, impermeable blockage structures form in this area. By analyzing experimental images of biofilm structures at the later stages, as well as coupling fluid flow and porous medium, and the finite element simulation, we find that the biofilm detachment is correlated with the morphology and permeability (kb) (from 10-15 to 10-9 m2) of the biofilm. The simulations show that there are two modes of biofilm detachment, such as internal detachment and external erosion.

Application of filter media surface hydrophobic modification to reduce bioclogging in the infiltration system

Bioclogging is a commonly encountered operational issue that lowers hydraulic conductivity and the overall performance of the infiltration systems. In this paper, a novel processing for alleviating bioclogging by filter media surface hydrophobic modification was presented. Two-dimensional porous media cells were used to observe the influence of hydrophobic modification on biofilm growth in the pore structure. Moreover, two continuous-flow columns packed with gravel, one of which half gravel was hydrophobically modified, were operated with artificial wastewater to verify the effect of hydrophobic modification on bioclogging alleviation. The results showed that the biofilm growth in the cell with hydrophobic modification was slow, and the biomass was less and liable to wipe off after hydrophobic treatment. Meanwhile, the hydraulic efficiency of the flow seepage field was also improved after hydrophobic treatment. The column tests results showed that the hydraulic conductivity of the filter bed with hydrophobic modification (Column B) decreased more slowly than that of another without hydrophobic modification (Column A). Column B had the hydraulic conductivity (k) of 0.66 cm/s in the final stage of the experiment, while the k of Column A was 0.14 cm/s. It verified that hydrophobic modification of partial filter media can alleviate the bioclogging problem of the infiltration systems to some extent. The results provide a new idea and potential technical support for solving bioclogging problem.

Fluid transport in porous media based on differences in filter media morphology and biofilm growth in bioreactors

To elucidate the effect of pore structure on bioclogging and seepage flow in bioreactors, we used X-ray computed tomography (X-CT) to investigate the changes in seepage flow of porous media in zeolite, gravel and ceramsite bioreactors with biofilm growth by injecting a non-ionic contrast medium iohexol. Based on the X-CT images using a ball-and-stick model, the highest average pore radius (R‾) and the average pore throat radius (r‾) in the ceramsite column were found under the initial conditions, which facilitated its permeability. The pore and throat of the gravel column were small and homogeneous relatively. Biofilm growth decreased the pore and pore throat in the columns. The total throat area of zeolite, gravel and ceramsite columns declined by 74%, 73% and 79% respectively. The zeolite column had the highest average pore throat, which contributed to its maximum conductivity subsequently after biofilm growth. Further, the fractal dimensions of the pore structure increased with biofilm growth, especially in the zeolite and ceramsite columns. The heterogeneity of the porous media was reinforced by the biofilm growth in the zeolite and ceramsite columns due to their higher heterogeneity initially. We also observed that an increase in heterogeneity of porous medium amplified the preferential flow and flow heterogeneities, especially in the zeolite and ceramsite columns.

Designs and methodologies to recreate in vitro human gut microbiota models

The human gut microbiota is widely considered to be a metabolic organ hidden within our bodies, playing a crucial role in the host’s physiology. Several factors affect its composition, so a wide variety of microbes residing in the gut are present in the world population. Individual excessive imbalances in microbial composition are often associated with human disorders and pathologies, and new investigative strategies to gain insight into these pathologies and define pharmaceutical therapies for their treatment are needed. In vitro models of the human gut microbiota are commonly used to study microbial fermentation patterns, community composition, and host-microbe interactions. Bioreactors and microfluidic devices have been designed to culture microorganisms from the human gut microbiota in a dynamic environment in the presence or absence of eukaryotic cells to interact with. In this review, we will describe the overall elements required to create a functioning, reproducible, and accurate in vitro culture of the human gut microbiota. In addition, we will analyze some of the devices currently used to study fermentation processes and relationships between the human gut microbiota and host eukaryotic cells.

Graphic abstract

A microfluidic platform for characterizing the structure and rheology of biofilm streamers

Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults. When ambient flow is present, this viscoelastic scaffold can take a streamlined shape, forming biofilm filaments suspended in flow, called streamers. Streamers significantly disrupt the fluid flow by causing rapid clogging and affect transport in aquatic environments. Despite their relevance, the structural and rheological characterization of biofilm streamers is still at an early stage. In this work, we present a microfluidic platform that allows the reproducible growth of biofilm streamers in controlled physico-chemical conditions and the characterization of their biochemical composition, morphology, and rheology in situ. We employed isolated micropillars as nucleation sites for the growth of single biofilm streamers under the continuous flow of a diluted bacterial suspension. By combining fluorescent staining of the EPS components and epifluorescence microscopy, we were able to characterize the biochemical composition and morphology of the streamers. Additionally, we optimized a protocol to perform hydrodynamic stress tests in situ, by inducing controlled variations of the fluid shear stress exerted on the streamers by the flow. Thus, the reproducibility of the formation process and the testing protocol make it possible to perform several consistent experimental replicates that provide statistically significant information. By allowing the systematic investigation of the role of biochemical composition on the structure and rheology of streamers, this platform will advance our understanding of biofilm formation.

Multi-scale model of clogging in microfluidic devices with grid-like geometries

We propose a coarse-grained theoretical model to capture the ageing of microfluidic devices under different conditions including constant applied flow rate and constant applied pressure gradient. Microfluidic devices that sort cells by their deformability hold significant promise for medical applications. However, clogging in these microfluidic systems causes their properties to change over time and potentially limits their reliability. We compare the results of the coarse-grained model with those of stochastic simulations and with existing theoretical studies. Lastly, we apply the model to experimental data on the clogging of sickle red blood cells and discuss its wider applicability.

Understanding the effects of aerodynamic and hydrodynamic shear forces on Pseudomonas aeruginosa biofilm growth

Biofilms are communities of bacterial cells encased in a self-produced polymeric matrix and exhibit high tolerance towards environmental stress. Despite the plethora of research on biofilms, most biofilm models are produced using mono-interface culture in static flow conditions, and knowledge of the effects of interfaces and mechanical forces on biofilm development remains fragmentary. This study elucidated the effects of air-liquid (ALI) or liquid-liquid (LLI) interfaces and mechanical shear forces induced by airflow and hydrodynamic flow on biofilm growing using a custom-designed dual-channel microfluidic platform. Results from this study showed that comparing biofilms developed under continuous nutrient supply and shear stresses free condition to those developed with limited nutrient supply, ALI biofilms were four times thicker, 60% less permeable, and 100 times more resistant to antibiotics, while LLI biofilms were two times thicker, 20% less permeable, and 100 times more resistant to antibiotics. Subjecting the biofilms to mechanical shear stresses affected the biofilm structure across the biofilm thickness significantly, resulting in generally thinner and denser biofilm compared to their controlled biofilm cultured in the absence of shear stresses, and the ALI and LLI biofilm's morphology was vastly different. Biofilms developed under hydrodynamic shear stress also showed increased antibiotic resistance. These findings highlight the importance of investigating biofilm growth and its mechanisms in realistic environmental conditions and demonstrate a feasible approach to undertake this work using a novel platform. This article is protected by copyright. All rights reserved.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Bacterial streamers as colloidal systems: Five grand challenges

Bacteria can thrive in biofilms, which are intricately organized communities with cells encased in a self-secreted matrix of extracellular polymeric substances (EPS). Imposed hydrodynamic stresses can transform this active colloidal dispersion of bacteria and EPS into slender thread-like entities called streamers. In this perspective article, the reader is introduced to the world of such deformable 'bacteria-EPS' composites that are a subclass of the generic flow-induced colloidal structures. While bacterial streamers have been shown to form in a variety of hydrodynamic conditions (turbulent and creeping flows), its abiotic analogues have only been demonstrated in low Reynolds number (Re < 1) particle-laden polymeric flows. Streamers are relevant to a variety of situations ranging from natural formations in caves and river beds to clogging of biomedical devices and filtration membranes. A critical review of the relevant biophysical aspects of streamer formation phenomena and unique attributes of its material behavior are distilled to unveil five grand scientific challenges. The coupling between colloidal hydrodynamics, device geometry and streamer formation are highlighted.

Towards Microfluidic-Based Exosome Isolation and Detection for Tumor Therapy

Exosomes are a class of cell-secreted, nano-sized extracellular vesicles with a bilayer membrane structure of 30-150 nm in diameter. Their discovery and application have brought breakthroughs in numerous areas, such as liquid biopsies, cancer biology, drug delivery, immunotherapy, tissue repair, and cardiovascular diseases. Isolation of exosomes is the first step in exosome-related research and its applications. Standard benchtop exosome separation and sensing techniques are tedious and challenging, as they require large sample volumes, multi-step operations that are complex and time-consuming, requiring cumbersome and expensive instruments. In contrast, microfluidic platforms have the potential to overcome some of these limitations, owing to their high-precision processing, ability to handle liquids at a microscale, and integrability with various functional units, such as mixers, actuators, reactors, separators, and sensors. These platforms can optimize the detection process on a single device, representing a robust and versatile technique for exosome separation and sensing to attain high purity and high recovery rates with a short processing time. Herein, we overview microfluidic strategies for exosome isolation based on their hydrodynamic properties, size filtration, acoustic fields, immunoaffinity, and dielectrophoretic properties. We focus especially on advances in label-free isolation of exosomes with active biological properties and intact morphological structures. Further, we introduce microfluidic techniques for the detection of exosomal proteins and RNAs with high sensitivity, high specificity, and low detection limits. We summarize the biomedical applications of exosome-mediated therapeutic delivery targeting cancer cells. To highlight the advantages of microfluidic platforms, conventional techniques are included for comparison. Future challenges and prospects of microfluidics towards exosome isolation applications are also discussed. Although the use of exosomes in clinical applications still faces biological, technical, regulatory, and market challenges, in the foreseeable future, recent developments in microfluidic technologies are expected to pave the way for tailoring exosome-related applications in precision medicine.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

Organic redox-active crystalline layers for reagent-free electrochemical antibiotic susceptibility testing (ORACLE-AST)

Rapid antibiotic susceptibility testing (AST) is critical in determining bacterial resistance or susceptibility to a particular antibiotic. Simple-to-use phenotype-based AST platforms can assist care-givers in timely prescription of the right antibiotic. Monitoring the change of bacterial viability by measuring electrochemical Faradaic current is a promising approach for rapid AST. However, the existing works require mixing redox-active reagents in the solution which can interfere with the antibiotics. In this paper, we developed a facile electrodeposition process for creating a redox-active crystalline layer (denoted as RZx) on pyrolytic graphite sheets (PGS), which was then utilized as the sensing layer for reagent-free electrochemical AST. To demonstrate the proof-of-principle, we tested the sensors with Escherichia coli (E. coli) K-12 treated with two antibiotics, ampicillin and kanamycin. While the sensors enable detection of bacterial metabolism mainly due to pH-sensitivity of RZx (∼ 53 mV/pH), secreted redox-active metabolites/compounds from whole cells are likely contributing to the signal as well. By monitoring the differential voltammetric signals, the sensors enable accurate prediction of the minimum inhibitory concentration (MIC) in 60 min (p < 0.03). The sensors are stable after 60 days storage in ambient conditions and enable analysis of microbial viability in complex solutions, as demonstrated in spiked milk and human whole blood.

Label-Free Electrochemical Microfluidic Chip for the Antimicrobial Susceptibility Testing

The emergence and spread of antibiotic-resistant bacteria is a global threat to human health. An accurate antibiotic susceptibility test (AST) before initiating the treatment is paramount in the treatment and bacterial resistance control. However, the current AST methods either are complex, use chemical and biological labels, lack multiplexing, are expensive, or are too slow to be used for routine screening. The primary objective of the current study is to develop an automated electrochemical microfluidic chip (EMC) for simple and rapid AST. The microfluidic channels and gold microelectrodes were designed for the automation of antibiotic mixing and distribution in multiple test chambers and for electrical signal measurements. The designed chip was tested for AST with E. coli samples, and the results were compared with conventional broth microdilution. The presented EMC provided rapid bacterial count and AST in 170 and 150 min, respectively, while the conventional broth microdilution evaluates in 450 and 240 min, respectively. The rapid AST capability of the EMC was further demonstrated with the artificial urine samples, and the results were obtained in 270 min, which was 90 min faster than the broth microdilution method. Additionally, the minimum inhibitory concentration (MIC) was evaluated on the EMC and compared with the results from an AlamarBlue assay. The experimental results indicate the sensitivity of the chip, minimum loss of antibiotics, and eventually, reduction in the evolution of antibiotic resistance. Cumulatively, we have developed an automated, label-free, economical, rapid, robust, and user-friendly EMC for the evaluation of AST in urine samples.

Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments

Biofilms regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages. This is evidence for architectural plasticity. Architectural plasticity allowed for complementary use of the space provided by the grain–pore complexes, which increased biofilm carrying capacity at the larger scale of the porous system. This increase comes potentially at the cost of a tradeoff. Contrasting time scales of oxygen replenishment and consumption, we show that streamers locally inhibit the growth of the BB downstream from the grains. Our study provides first insights into the biophysical underpinnings to the success of multispecies biofilms in porous environments.

Microfluidic bioanalytical flow cells for biofilm studies: a review

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.

Impact of bacterial streamers on biofouling of microfluidic filtration systems

We investigate the effect of biofouling in a microfluidic filtration system. The microfluidic platform consists of cylindrical microposts with a pore-spacing of 2 μm, which act as the filtration section of the device. One of our key findings is that there exists a critical pressure difference above which pronounced streamer formation is observed, which eventually leads to rapid clogging of the device with an accompanying exponential decrease in permeate flow. Moreover, when streamers do form, de-clogging of pores also occurs intermittently, which leads to small time scale fluctuations [O(10¹ s)] superimposed upon the large time scale [O(10² min)] clogging of the system. These de-clogging phenomena lead to a sharp increase in water permeation through the microfluidic filtration device but rates the water quality as biomass debris is transported in the permeate. Streamer-based clogging shares similarities with various fouling mechanisms typically associated with membranes. Finally, we also show that the pH of the feed strongly affects biofouling of the microfluidic filtration system.

Nano-Enabled Approaches to Chemical Imaging in Biosystems

Understanding and predicting how biosystems function require knowledge about the dynamic physicochemical environments with which they interact and alter by their presence. Yet, identifying specific components, tracking the dynamics of the system, and monitoring local environmental conditions without disrupting biosystem function present significant challenges for analytical measurements. Nanomaterials, by their very size and nature, can act as probes and interfaces to biosystems and offer solutions to some of these challenges. At the nanoscale, material properties emerge that can be exploited for localizing biomolecules and making chemical measurements at cellular and subcellular scales. Here, we review advances in chemical imaging enabled by nanoscale structures, in the use of nanoparticles as chemical and environmental probes, and in the development of micro- and nanoscale fluidic devices to define and manipulate local environments and facilitate chemical measurements of complex biosystems. Integration of these nano-enabled methods will lead to an unprecedented understanding of biosystem function.

Confined Flow: Consequences and Implications for Bacteria and Biofilms

Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.

Abiotic streamers in a microfluidic system

In this work, we report the phenomenon of formation of particle aggregates in the form of thin slender strings when a polyacrylamide (PAM) solution, laden with polystyrene (PS) beads is introduced into a microfluidic device containing an array of micropillars. PAM and a dilute solution of PS beads are introduced into the microfluidic channel through two separate inlets and localized particle aggregation is found to occur under certain flow regimes. The particle aggregates initially have a string-like morphology and are tethered at their ends to the micropillar walls, while the structure remains suspended in the fluid medium. Such a morphology inspired us to name these structures streamers. The flow regimes under which streamer formation is observed are quantified through state diagrams. We discuss the streamer formation time-scales and also show that streamer formation is likely the result of the flocculation of PS beads. Streamer formation has implications in investigating particle-laden complex flows through porous media.

A new look at bubbles during biofilm inoculation reveals pronounced effects on growth and patterning

Specially designed microfluidic bioflow cells were used to temporarily trap microbubbles during different inoculation stages of Pseudomonas sp. biofilms. Despite being eliminated many hours before biofilm appearance, templated growth could occur at former bubble positions. Bubble-templated growth was either continuous or in ring patterns, depending on the stage of inoculation when the bubbles were introduced. Templated biofilms were strongly enhanced in terms of their growth kinetics and structural homogeneity. High resolution confocal imaging showed two separate bubble-induced bacterial trapping modes, which were responsible for the altered biofilm development. It is concluded that static bubbles can be exploited for fundamental improvements to bioreactor performance, as well as open new avenues to study isolated bacteria and small colonies.

Using micro-patterned surfaces to inhibit settlement and biofilm formation by Bacillus subtilis

Biofilm is a biological complex caused by bacteria attachment to the substrates and their subsequent reproduction and secretion. This phenomenon reduces heat transfer efficiency and causes significant losses in treated sewage heat-recovering systems. This paper describes a physical approach to inhibit bacteria settlement and biofilm formation by Bacillus subtilis, which is the dominant species in treated sewage. Here, micro-patterned surfaces with different characteristics (stripe and cube) and dimensions (1-100 μm) were fabricated as surfaces of interest. Model sewage was prepared and a rotating coupon device was used to form the biofilms. Precision balance, scanning electron microscopy, and confocal laser scanning microscopy (CLSM) were employed to investigate the inhibitory effects and the mechanisms of the biofilm-surface interactions. The results have shown that surfaces with small pattern sizes (1 and 2 μm) all reduced biofilm formation significantly. Interestingly, the CLSM images showed that the surfaces do not play a role in "killing" the bacteria. These findings are useful for future development of new process surfaces on which bacteria settlement and biofilm formation can be inhibited or minimized.