The Design of Simple Bacterial Microarrays: Development towards Immobilizing Single Living Bacteria on Predefined Micro-Sized Spots on Patterned Surfaces

Bacterial Patterning: A Promising Biofabrication Technique

Bacterial patterning has emerged as a pivotal biofabrication technique in the biomedical field. In the past 2 decades, a diverse array of bacterial patterning approaches have been developed to enable the precise manipulation of the spatial distribution of bacterial patterns for various applications. Despite the significance of these advancements, there is a deficiency of review articles providing an overview of bacterial patterning technologies. In this mini-review, we systematically summarize the progress of bacterial patterning over the past 2 decades. This review commences with an elucidation of the definition and fundamental principles of bacterial patterning. Subsequently, we introduce the established bacterial patterning strategies, accompanied by discussions about the advantages and limitations of each approach. Furthermore, we showcase the biomedical applications of these strategies, highlighting their efficacy in spatial control of biofilms, biosensing, and biointervention. Finally, this mini-review is concluded with a summary and an outlook on future challenges and opportunities. It is anticipated that this mini-review can serve as a concise guide for those who are interested in this exciting and rapidly evolving research area.

Low-cost gel-filled microwell array device for screening marine microbial consortium

In order to exploit the microbes present in the environment for their beneficial resources, effective selection and isolation of microbes from environmental samples is essential. In this study, we fabricated a gel-filled microwell array device using resin for microbial culture. The device has an integrated sealing mechanism that enables high-density isolation based on the culture of microorganisms; the device is easily manageable, facilitating observation using bright-field microscopy. This low-cost device made from polymethyl methacrylate (PMMA)/polyethylene terephthalate (PET) has 900 microwells (600 μm × 600 μm × 700 μm) filled with a microbial culture gel medium in glass slide-sized plates. It also has grooves for maintaining the moisture content in the micro-gel. The partition wall between the wells has a highly hydrophobic coating to inhibit microbial migration to neighboring wells and to prevent exchange of liquid substances. After being hermetically sealed, the device can maintain moisture in the agarose gels for 7 days. In the bacterial culture experiment using this device, environmental bacteria were isolated and cultured in individual wells after 3 days. Moreover, the isolated bacteria were then picked up from wells and re-cultured. This device is effective for the first screening of microorganisms from marine environmental samples.

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation

The morphological plasticity of bacteria to form filamentous cells commonly represents an adaptive strategy induced by stresses. In contrast, for diverse human and plant pathogens, filamentous cells have been recently observed during biofilm formation, but their functions and triggering mechanisms remain unclear. To experimentally identify the underlying function and hypothesized cell communication triggers of such cell morphogenesis, spatially controlled cell patterning is pivotal. Here, we demonstrate highly selective cell adhesion of the biofilm-forming phytopathogen Xylella fastidiosa to gold-patterned SiO₂ substrates with well-defined geometries and dimensions. The consequent control of both cell density and distances between cell clusters demonstrated that filamentous cell formation depends on cell cluster density, and their ability to interconnect neighboring cell clusters is distance-dependent. This process allows the creation of large interconnected cell clusters that form the structural framework for macroscale biofilms. The addition of diffusible signaling molecules from supernatant extracts provides evidence that cell filamentation is induced by quorum sensing. These findings and our innovative platform could facilitate therapeutic developments targeting biofilm formation mechanisms of X. fastidiosa and other pathogens.

Biopolymer Patterning-Directed Secretion in Mucoid and Nonmucoid Strains of Pseudomonas aeruginosa Revealed by Multimodal Chemical Imaging

Quinolone, pyocyanin, and rhamnolipid production were studied in Pseudomonas aeruginosa by spatially patterning mucin, a glycoprotein important to infection of lung epithelia. Mass spectrometric imaging and confocal Raman microscopy are combined to probe P. aeruginosa biofilms from mucoid and nonmucoid strains grown on lithographically defined patterns. Quinolone signatures from biofilms on patterned vs unpatterned and mucin vs mercaptoundecanoic acid (MUA) surfaces were compared. Microbial attachment is accompanied by secretion of 2-alkyl-4-quinolones as well as rhamnolipids from the mucoid and nonmucoid strains. Pyocyanin was also detected both in the biofilm and in the supernatant in the mucoid strain only. Significant differences in the spatiotemporal distributions of secreted factors are observed between strains and among different surface patterning conditions. The mucoid strain is sensitive to composition and patterning while the nonmucoid strain is not, and in promoting community development in the mucoid strain, nonpatterned surfaces are better than patterned, and mucin is better than MUA. Also, the mucoid strain secretes the virulence factor pyocyanin in a way that correlates with distress. A change in the relative abundance for two rhamnolipids is observed in the mucoid strain during exposure to mucin, whereas minimal variation is observed in the nonmucoid strain. Differences between mucoid and nonmucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected and withdrawn biofilms that achieve Pseudomonas quinolone signal production under limited conditions.

Effect of design geometry, exposure energy, cytophilic molecules, cell type and load in fabrication of single-cell arrays using micro-contact printing

In this study a range of factors influencing the fabrication of single-cell arrays (SCAs) are identified and investigated. Micro-contact printing was used to introduce spots coated with polyethyleneimine or Matrigel on glass surfaces pre-coated with polyethylene glycol. Unmodified E. coli, Synechococcus sp., Chlamydomonas reinhardtii as well as diverse mammalian cells including HUVEC, AAV293, U87, OHS, PC3, SW480, HepG2 and AY-27 were successfully immobilised onto the chemically coated spots. The developed SCAs show high cell viability and probability for capturing single-cells. A discrepancy between the size and shape of the squares described in the design file and the actual structures obtained in the final PDMS structure is characterised and quantified. The discrepancy is found to be depending on the exposure energy used in the photolithography process as well as the size of the squares and their separation distance as detailed in the design file. In addition to these factors, the effect of the cell density loaded onto the patterned surfaces is also characterised. The systematic characterisation of key parameters that need to be optimised prior to the fabrication of SCAs is essential in order to increase the efficiency and reproducibility of future fabrication of SCAs for single-cell studies.

Conformal Bacterial Cellulose Coatings as Lubricious Surfaces

We report a versatile method to form bacterial cellulose coatings through simple dip-coating of 3D objects in suspensions of cellulose-producing bacteria. The adhesion of cellulose-secreting bacteria on objects was promoted through surface roughness and chemistry. Immobilized bacteria secreted highly porous hydrogels with high water content directly from the surface of a variety of materials. The out-of-plane orientation of cellulose fibers present in this coating leads to high mechanical stability and energy dissipation with minimal cellulose concentration. The conformal, biocompatible, and lubricious nature of the in situ grown cellulose surfaces makes the coated 3D objects attractive for biomedical applications.

Pathogen-Imprinted Organosiloxane Polymers as Selective Biosensors for the Detection of Targeted E. coli

Early detection of pathogens requires methods that are fast, selective, sensitive and affordable. We report the development of a biosensor with high sensitivity and selectivity based on the low-cost preparation of organosiloxane (OSX) polymers imprinted with E. coli-GFP (green fluorescent protein). OSX polymers with high optical transparency, no cracking, and no shrinkage were prepared by varying several parameters of the sol-gel reaction. The unique shape and chemical fingerprint of the targeted inactivated E. coli-GFP were imprinted into bulk polymers by replication imprinting where the polymer solution was dropcast onto a bacteria template that produced a replica of the bacterial shape and chemistry on the polymer surface upon removal of the template. Capture performances were studied under non-laminar flow conditions with samples containing inactivated E. coli-GFP and compared to inactivated S. typhimurium-GFP. Capture selectivity ratios are dependent on the type of alkoxysilanes used, the H2O:silane molar ratio, and the polymerization temperature. The bacteria concentration in suspension ranged from ~6 × 105 to 1.6 × 109 cells/mL. E. coli-imprinted OSX polymers with polyethylene glycol (PEG) differentiated between the targeted bacterium E. coli, and non-targeted bacteria S. typhimurium and native E. coli-GFP, achieving selectivity ratios up to 4.5 times higher than polydimethylsiloxane (PDMS) and OSX polymers without PEG.

Cell biology of microbes and pharmacology of antimicrobial drugs explored by Atomic Force Microscopy

Antimicrobial molecules have been used for more than 50 years now and are the basis of modern medicine. No surgery can nowdays be imagined to be performed without antibiotics; dreadful diseases like tuberculosis, leprosis, siphilys, and more broadly all microbial induced diseases, can be cured only through the use of antimicrobial treatments. However, the situation is becoming more and more complex because of the ability of microbes to adapt, develop, acquire, and share mechanisms of resistance to antimicrobial agents. We choose to introduce this review by briefly drawing the panorama of antimicrobial discovery and development, but also of the emergence of microbial resistance. Then we describe how Atomic Force Microscopy (AFM) can be used to provide a better understanding of the mechanisms of action of these drugs at the nanoscale level on microbial interfaces. In this section, we will address these questions: (1) how does drug treatment affect the morphology of single microbes?; (2) do antimicrobial molecules modify the nanomechanical properties of microbes, or do the nanomechanical properties of microbes play a role in antimicrobial activity and efficiency?; and (3) how are the adhesive abilitites of microbes affected by antimicrobial drugs treatment? Finally, in a second part of this review we focus on recent studies aimed at changing the paradigm of the single molecule/cell technology that AFM typically represents. Recent work dealing with the creation of a microbe array which can be explored by AFM will be presented, as these developments constitute the first steps toward transforming AFM into a higher throughput technology. We also discuss papers using AFM as NanoMechnanicalSensors (NEMS), and demonstrate the interest of such approaches in clinical microbiology to detect quickly and with high accuracy microbial resistance.

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.

Heterogeneity in GFP expression in isogenic populations of P. putida KT2440 investigated using flow cytometry and bacterial microarrays

Fluorescence intensities were determined using both flow cytometry and bacterial microarrays for Pseudomonas putida expressing GFP upon addition of an inducer. Fluorescence micrographs revealed static inter-cell differences in fluorescence emission.

Microarrays for the study of compartmentalized microorganisms in alginate microbeads and (W/O/W) double emulsions

Here, we present two array platforms for small (50–100 μm) cell-containing 3D compartments prepared by droplet-based microfluidics.