Antibody selection for immobilizing living bacteria

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.

Biotrapping Ureolytic Bacteria on Sand to Improve the Efficiency of Biocementation

Microbially induced calcium carbonate precipitation (MICP) has emerged as a novel technology with the potential to produce building materials through lower-temperature processes. The formation of calcium carbonate bridges in MICP allows the biocementation of aggregate particles to produce biobricks. Current approaches require several pulses of microbes and mineralization media to increase the quantity of calcium carbonate minerals and improve the strength of the material, thus leading to a reduction in sustainability. One potential technique to improve the efficiency of strength development involves trapping the bacteria on the aggregate surfaces using silane coupling agents such as positively charged 3-aminopropyl-methyl-diethoxysilane (APMDES). This treatment traps bacteria on sand through electrostatic interactions that attract negatively charged walls of bacteria to positively charged amine groups. The APMDES treatment promoted an abundant and immediate association of bacteria with sand, increasing the spatial density of ureolytic microbes on sand and promoting efficient initial calcium carbonate precipitation. Though microbial viability was compromised by treatment, urea hydrolysis was minimally affected. Strength was gained much more rapidly for the APMDES-treated sand than for the untreated sand. Three injections of bacteria and biomineralization media using APMDES-treated sand led to the same strength gain as seven injections using untreated sand. The higher strength with APMDES treatment was not explained by increased calcium carbonate accrual in the structure and may be influenced by additional factors such as differences in the microstructure of calcium carbonate bridges between sand particles. Overall, incorporating pretreatment methods, such as amine silane coupling agents, opens a new avenue in biomineralization research by producing materials with an improved efficiency and sustainability.

Long-Period Gratings and Microcavity In-Line Mach Zehnder Interferometers as Highly Sensitive Optical Fiber Platforms for Bacteria Sensing

Selected optical fiber sensors offer extraordinary sensitivity to changes in external refractive (RI), which make them promising for label-free biosensing. In this work the most sensitive ones, namely long-period gratings working at (DTP-LPG) and micro-cavity in-line Mach-Zehnder interferometers (µIMZI) are discussed for application in bacteria sensing. We describe their working principles and RI sensitivity when operating in water environments, which is as high as 20,000 nm/RIU (Refractive index unit) for DTP-LPGs and 27,000 nm/RIU for µIMZIs. Special attention is paid to the methods to enhance the sensitivity by etching and nano-coatings. While the DTP-LPGs offer a greater interaction length and sensitivity to changes taking place at their surface, the µIMZIs are best suited for investigations of sub-nanoliter and picoliter volumes. The capabilities of both the platforms for bacteria sensing are presented and compared for strains of Escherichia coli, lipopolysaccharide E. coli, outer membrane proteins of E. coli, and Staphylococcus aureus. While DTP-LPGs have been more explored for bacteria detection in 10²–10⁶ Colony Forming Unit (CFU)/mL for S. aureus and 10³–10⁹ CFU/mL for E. coli, the µIMZIs reached 10²–10⁸ CFU/mL for E. coli and have a potential for becoming picoliter bacteria sensors.

From molecules to multispecies ecosystems: the roles of structure in bacterial biofilms

Biofilms are communities of sessile microbes that are bound to each other by a matrix made of biopolymers and proteins. Spatial structure is present in biofilms on many lengthscales. These range from the nanometer scale of molecular motifs to the hundred-micron scale of multicellular aggregates. Spatial structure is a physical property that impacts the biology of biofilms in many ways. The molecular structure of matrix components controls their interaction with each other (thereby impacting biofilm mechanics) and with diffusing molecules such as antibiotics and immune factors (thereby impacting antibiotic tolerance and evasion of the immune system). The size and structure of multicellular aggregates, combined with microbial consumption of growth substrate, give rise to differentiated microenvironments with different patterns of metabolism and gene expression. Spatial association of more than one species can benefit one or both species, while distances between species can both determine and result from the transport of diffusible factors between species. Thus, a widespread theme in the biological importance of spatial structure in biofilms is the effect of structure on transport. We survey what is known about this and other effects of spatial structure in biofilms, from molecules up to multispecies ecosystems. We conclude with an overview of what experimental approaches have been developed to control spatial structure in biofilms and how these and other experiments can be complemented with computational work.

Isolation and separation of Listeria monocytogenes using bacteriophage P100-modified magnetic particles

A bacteriophage-assisted magnetic separation method was developed for the isolation of Listeria monocytogenes from complex food matrices. The aim of this study is to understand the effect of phage immobilization methods and the magnetic particle sizes on the phage coupling and infectivity retention of the magnetic particles. In this study, bacteriophage P100-modified magnetic particles (PMMPs) were developed for the separation of L. monocytogenes from food matrices. Three sizes of magnetic particles (MP) (150 nm, 500 nm, and 1 μm) were used for phage immobilization via chemical and physical methods. The coupling ratio of phage was investigated, and the performance of each PMMP complex was evaluated by their L. monocytogenes capture efficiency. When compared to the chemical immobilization method, the physically immobilized PMMP complex achieved a higher capture efficiency initially, with excellent selectivity towards target bacteria. The PMMPs were further tested for selective isolation of L. monocytogenes using real food samples such as ground beef and whole milk.

Time-Resolved Imaging of Bacterial Surfaces Using Atomic Force Microscopy

Time-resolved atomic force microscopy (AFM) offers countless new modes by which to study bacterial cell physiology on relevant time scales, from mere milliseconds to hours and days on end. In addition, time-lapse AFM acts as a complementary tool to optical fluorescence microscopy (OFM), for which the combination offers a correlative link between the physical manifestation of bacterial phenotypes and molecular mechanisms obeying those principles. Herein we describe the essential materials and methods necessary for conducting time-resolved AFM and dual AFM/OFM experiments on bacteria.

Detecting ligand interactions in real time on living bacterial cells

Time-resolved analysis assays of receptor-ligand interactions are fundamental in basic research and drug discovery. Adequate methods are well developed for the analysis of recombinant proteins such as antibody-antigen interactions. However, assays for time-resolved ligand-binding processes on living cells are still rare, in particular within microbiology. In this report, the real-time cell-binding assay (RT-CBA) technology LigandTracer®, originally designed for mammalian cell culture, was extended to cover Gram-positive and Gram-negative bacteria. This required the development of new immobilization methods for bacteria, since LigandTracer depends on cells being firmly attached to a Petri dish. The evaluated Escherichia coli CJ236 and BL21 as well as Staphylococcus carnosus TM300 strains were immobilized to plastic Petri dishes using antibody capture, allowing us to depict kinetic binding traces of fluorescently labeled antibodies directed against surface-displayed bacterial proteins for as long as 10–15 h. Interaction parameters, such as the affinity and kinetic constants, could be estimated with high precision (coefficient of variation 9–44%) and the bacteria stayed viable for at least 16 h. The other tested attachment protocols were inferior to the antibody capture approach. Our attachment protocol is generic and could potentially also be applied to other assays and purposes.

Plasma nanotextured polymeric lab-on-a-chip for highly efficient bacteria capture and lysis

We describe the design, fabrication, and successful demonstration of a sample preparation module comprising bacteria cell capture and thermal lysis on-chip with potential applications in food sample pathogen analysis. Plasma nanotexturing of the polymeric substrate allows increase of the surface area of the chip and the antibody binding capacity. Three different anti-Salmonella antibodies were directly and covalently linked to plasma treated chips without any additional linker chemistry or other treatment. Then, the Ab-modified chips were tested for their capacity to bind bacteria in the concentration range of 10(2)-10(8) cells per mL; the module exhibited 100% efficiency in Salmonella enterica serovar Typhimurium bacteria capture for cell suspensions below 10(5) cells per mL (10(4) cells injected with a 100 μL sample volume) and efficiency higher than 50% for 10(7) cells per mL. Moreover, thermal lysis achieved on-chip from as low as 10 captured cells was demonstrated and shown to compare well with off-chip lysis. Excellent selectivity (over 1 : 300) was obtained in a sample containing, in addition to S. Typhimurium and E. coli bacteria.

Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome's potential to cause inflammation

Immunodeficiencies can lead to alterations of the gut microbiome that render it pathogenic and capable of transmitting disease to naïve hosts. Here, we review the role of Toll-like receptor (TLR) 5, the innate receptor for bacterial flagellin, in immune responses to the normal gut microbiota with a focus its role on adaptive immunity. Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5(-/-) host. A variety of human TLR5 gene alleles exist that also associated with inflammatory conditions and may do so via effects on the gut microbiome and altered host-microbial crosstalk.

Sharp transition in the immunoimmobilization of E. coli O157:H7

This work focuses on immobilization of living enterohemorrhagic Escherichia coli O157:H7 on a gold surface as a function of the concentration of antibody tethered to the surface in the physiological environment of the organisms. Experiments are conducted using antibodies raised against bacterial surface lipopolysaccharides (LPS) tethered to gold-coated silicon wafers at surface concentrations spanning a range from submonolayers of antibodies to full coverage, an estimated 1 antibody per ∼100 nm(2). A careful optimization of surface chemistry is conducted to obtain the most efficient tethering of the antibodies to the surface. The mechanism of immobilizing the bacteria is antibody-antigen interactions between the tethered antibodies on the surface and the bacterial surface LPS firmly attached to the bacteria. This type of attachment is known as immunoimmobilization. The experiments suggest no noticeable bacterial attachment until the surface antibody concentration reaches ∼70% of a full monolayer of coverage. Above this critical antibody density, a sharp increase in immunoimmobilized bacteria is observed as they populate nearly 80% to 100% of the available surface area, reaching ∼1.2 cells/10 μm(2). This sharp increase in population is tentatively explained in terms of the minimum number of antibody-antigen interactions required per bacterium to immobilize the cell. This critical number is estimated to be ∼6000-8000 antibodies per bacterium (having a 1 μm(2) footprint on the surface) under the assumption that a full monolayer of antibodies is about 1 antibody per ∼100 nm(2). However, the large majority of the 6000-8000 antibodies are not expected to participate in antibody-antigen interactions, in that the loose LPS in solution will saturate many of these antibodies before bacteria have a chance to interact with them. Furthermore, the geometric considerations will further restrict the majority of the active antibodies from interacting with the surface antigens of the cell, reducing its effective contact area with the antibodies considerably.

Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut

Gut mucosal barrier breakdown and inflammation have been associated with high levels of flagellin, the principal bacterial flagellar protein. Although several gut commensals can produce flagella, flagellin levels are low in the healthy gut, suggesting the existence of control mechanisms. We find that mice lacking the flagellin receptor Toll-like receptor 5 (TLR5) exhibit a profound loss of flagellin-specific immunoglobulins (Igs) despite higher total Ig levels in the gut. Ribotyping of IgA-coated cecal microbiota showed Proteobacteria evading antibody coating in the TLR5(-/-) gut. A diversity of microbiome members overexpressed flagellar genes in the TLR5(-/-) host. Proteobacteria and Firmicutes penetrated small intestinal villi, and flagellated bacteria breached the colonic mucosal barrier. In vitro, flagellin-specific Ig inhibited bacterial motility and downregulated flagellar gene expression. Thus, innate-immunity-directed development of flagellin-specific adaptive immune responses can modulate the microbiome's production of flagella in a three-way interaction that helps to maintain mucosal barrier integrity and homeostasis.

Single-cell control of initial spatial structure in biofilm development using laser trapping

Biofilms are sessile communities of microbes that are spatially structured by an embedding matrix. Biofilm infections are notoriously intractable. This arises, in part, from changes in the bacterial phenotype that result from spatial structure. Understanding these interactions requires methods to control the spatial structure of biofilms. We present a method for growing biofilms from initiating cells whose positions are controlled with single-cell precision using laser trapping. The native growth, motility, and surface adhesion of positioned microbes are preserved, as we show for model organisms Pseudomonas aeruginosa and Staphylococcus aureus. We demonstrate that laser-trapping and placing bacteria on surfaces can reveal the effects of spatial structure on bacterial growth in early biofilm development.

Gold-Coated Iron Composite Nanospheres Targeted the Detection of Escherichia coli

We report the preparation and characterization of spherical core-shell structured Fe3O4-Au magnetic nanoparticles, modified with two component self-assembled monolayers (SAMs) consisting of 3-mercaptophenylboronic acid (3-MBA) and 1-decanethiol (1-DT). The rapid and room temperature synthesis of magnetic nanoparticles was achieved using the hydroxylamine reduction of HAuCl4 on the surface of ethylenediaminetetraacetic acid (EDTA)-immobilized iron (magnetite Fe3O4) nanoparticles in the presence of an aqueous solution of hexadecyltrimetylammonium bromide (CTAB) as a dispersant. The reduction of gold on the surface of Fe3O4 nanoparticles exhibits a uniform, highly stable, and narrow particle size distribution of Fe3O4-Au nanoparticles with an average diameter of 9 ± 2 nm. The saturation magnetization value for the resulting nanoparticles was found to be 15 emu/g at 298 K. Subsequent surface modification with SAMs against glucoside moieties on the surface of bacteria provided effective magnetic separation. Comparison of the bacteria capturing efficiency, by means of different molecular recognition agents 3-MBA, 1-DT and the mixed monolayer of 3-MBA and 1-DT was presented. The best capturing efficiency of E. coli was achieved with the mixed monolayer of 3-MBA and 1-DT-modified nanoparticles. Molecular specificity and selectivity were also demonstrated by comparing the surface-enhanced Raman scattering (SERS) spectrum of E. coli-nanoparticle conjugates with bacterial growth media.

Flagella overexpression attenuates Salmonella pathogenesis

Flagella are cell surface appendages involved in a number of bacterial behaviors, such as motility, biofilm formation, and chemotaxis. Despite these important functions, flagella can pose a liability to a bacterium when serving as potent immunogens resulting in the stimulation of the innate and adaptive immune systems. Previous work showing appendage overexpression, referred to as attenuating gene expression (AGE), was found to enfeeble wild-type Salmonella. Thus, this approach was adapted to discern whether flagella overexpression could induce similar attenuation. To test its feasibility, flagellar filament subunit FliC and flagellar regulon master regulator FlhDC were overexpressed in Salmonella enterica serovar Typhimurium wild-type strain H71. The results show that the expression of either FliC or FlhDC alone, and co-expression of the two, significantly attenuates Salmonella. The flagellated bacilli were unable to replicate within macrophages and thus were not lethal to mice. In-depth investigation suggests that flagellum-mediated AGE was due to the disruptive effects of flagella on the bacterial membrane, resulting in heightened susceptibilities to hydrogen peroxide and bile. Furthermore, flagellum-attenuated Salmonella elicited elevated immune responses to Salmonella presumably via FliC's adjuvant effect and conferred robust protection against wild-type Salmonella challenge.

Role of overexpressed CFA/I fimbriae in bacterial swimming

Enterotoxigenic Escherichia coli CFA/I is a protective antigen and has been overexpressed in bacterial vectors, such as Salmonella Typhimurium H683, to generate vaccines. Effects that overexpressed CFA/I may engender on the bacterial host remain largely unexplored. To investigate, we constructed a high CFA/I expression strain, H683-pC2, and compared it to a low CFA/I expression strain, H683-pC, and to a non-CFA/I expression strain, H683-pY. The results showed that H683-pC2 was less able to migrate into semisolid agar (0.35%) than either H683-pC or H683-pY. Bacteria that migrated showed motility halo sizes of H683-pC2 < H683-pC < H683-pY. In the liquid culture media, H683-pC2 cells precipitated to the bottom of the tube, while those of H683-pY did not. In situ imaging revealed that H683-pC2 bacilli tended to auto-agglutinate within the semisolid agar, while H683-pY bacilli did not. When the cfaBE fimbrial fiber encoding genes were deleted from pC2, the new plasmid, pC2(-), significantly recovered bacterial swimming capability. Our study highlights the negative impact of overexpressed CFA/I fimbriae on bacterial swimming motility.

Capture efficiency of Escherichia coli in fimbriae-mediated immunoimmobilization

Capturing pathogens on a sensor surface is one of the most important steps in the design of a biosensor. The efficiency of a biosensor at capturing pathogens has direct bearing on its sensitivity. In this work we investigated the capturing of Escherichia coli on substrates modified with antibodies targeting different types of fimbriae: K88ab (F4), K88ac (F4), K99 (F5), 987P (F6), F41, and CFA/I. The results suggest that all these fimbriae can be used for the efficient immobilization of living E. coli cells. The immobilization efficiency was affected by the purity and clone type of the antibody and the fimbriae expression level of the bacteria. For a specific fimbriae type, a higher immobilization efficiency was often observed with the monoclonal antibodies. Immunoimmobilization was utilized in an antibody microarray immersed in a mixed culture of pathogens to demonstrate the rapid and simultaneous label-free detection of multiple pathogens within less than 1 h using a single test. The capture rate of living pathogens exceeds a single bacterium per 100 × 100 μm(2) area per 0.5 h of incubation for a bulk concentration of 10(5) cfu/mL.

Development of a high-performance immunolatex based on "soft landing" antibody immobilization mechanism

Rabbit anti-human ferritin (anti-hFT) polyclonal immunoglobulin G (IgG) and poly(ethylene glycol) (PEG) were sequentially co-immobilized onto polystyrene submicroparticles (sMPs) to construct sMP/anti-hFT/PEG (SAP) immunolatex. Chemical immobilization of anti-hFT was performed at different pH levels to evaluate variations in antigen recognition. Basic pH disfavored conjugation of anti-hFT to sMPs, but remarkably increased its antigen recognition in comparison to that at neutral pH. We investigated this intriguing phenomenon further by assessing the kinetics of antibody binding, including the time-dependency of immobilization, antigen recognition, and orientation of bound anti-hFT. Therefore, we attributed high antigen recognition to significant electrostatic repulsion between sMPs and anti-hFT at basic pH, which predominately prevented anti-hFT access to sMPs and concurrently promoted anti-hFT orientations suitable for antigen recognition. Subsequent PEG modification maintained such anti-hFT orientation, without which antigen-accessible orientations would have decreased with time. Thus, properly oriented antibody and immediate PEGylation after antibody immobilization contributed to the formation of a high-performance SAP immunolatex.

Antibody purification-independent microarrays (PIM) by direct bacteria spotting on TiO2-treated slides

The preparation of effective conventional antibody microarrays depends on the availability of high quality material and on the correct accessibility of the antibody active moieties following their immobilization on the support slide. We show that spotting bacteria that expose recombinant antibodies on their external surface directly on nanostructured-TiO(2) or epoxy slides (purification-independent microarray - PIM) is a simple and reliable alternative for preparing sensitive and specific microarrays for antigen detection. Variable domains of single heavy-chain antibodies (VHHs) against fibroblast growth factor receptor 1 (FGFR1) were used to capture the antigen diluted in serum or BSA solution. The FGFR1 detection was performed by either direct antigen labeling or using a sandwich system in which FGFR1 was first bound to its antibody and successively identified using a labeled FGF. In both cases the signal distribution within each spot was uniform and spot morphology regular. The signal-to-noise ratio of the signal was extremely elevated and the specificity of the system was proved statistically. The LOD of the system for the antigen was calculated being 0.4ng/mL and the dynamic range between 0.4ng/mL and 10μg/mL. The microarrays prepared with bacteria exposing antibodies remain fully functional for at least 31 days after spotting. We finally demonstrated that the method is suitable for other antigen-antibody pairs and expect that it could be easily adapted to further applications such as the display of scFv and IgG antibodies or the autoantibody detection using protein PIMs.

Screening lectin-binding specificity of bacterium by lectin microarray with gold nanoparticle probes

To develop a novel high-throughput tool for monitoring specific affinity of microbes with lectins, a kind of lectin microarray has been fabricated by immobilizing lectins on epoxide-derivatized glass slides and used to capture microbes. The capturing events are marked by attachment of lectin-conjugated gold nanoparticles followed by silver deposition to enhance the resonance light scattering (RLS) of the particles. The interactions of 16 lectins with four bacteria and one fungus were profiled by this approach. We demonstrated that the gold-nanoparticle-labeled array was suitable for identifying the binding affinity of lectin with bacterium, as well as determining the bacterium with high sensitivity. More importantly, we found that the growth of microbial strains in different culture media resulted in significant changes in their binding affinities with lectins, which might be important to the pathogenesis of the organisms.

Application of atomic force microscopy in bacterial research

The atomic force microscope (AFM) has evolved from an imaging device into a multifunctional and powerful toolkit for probing the nanostructures and surface components on the exterior of bacterial cells. Currently, the area of application spans a broad range of interesting fields from materials sciences, in which AFM has been used to deposit patterns of thiol-functionalized molecules onto gold substrates, to biological sciences, in which AFM has been employed to study the undesirable bacterial adhesion to implants and catheters or the essential bacterial adhesion to contaminated soil or aquifers. The unique attribute of AFM is the ability to image bacterial surface features, to measure interaction forces of functionalized probes with these features, and to manipulate these features, for example, by measuring elongation forces under physiological conditions and at high lateral resolution (<1 A). The first imaging studies showed the morphology of various biomolecules followed by rapid progress in visualizing whole bacterial cells. The AFM technique gradually developed into a lab-on-a-tip allowing more quantitative analysis of bacterial samples in aqueous liquids and non-contact modes. Recently, force spectroscopy modes, such as chemical force microscopy, single-cell force spectroscopy, and single-molecule force spectroscopy, have been used to map the spatial arrangement of chemical groups and electrical charges on bacterial surfaces, to measure cell-cell interactions, and to stretch biomolecules. In this review, we present the fascinating options offered by the rapid advances in AFM with emphasizes on bacterial research and provide a background for the exciting research articles to follow.