Liquid transport facilitated by channels in Bacillus subtilis biofilms

Thermo-adaptive interfacial solar evaporation enhanced by dynamic water gating

Solar-driven evaporation offers a sustainable solution for water purification, but efficiency losses due to heat dissipation and fouling limit its scalability. Herein, we present a bilayer-structured solar evaporator (SDWE) with dynamic fluidic flow mechanism, designed to ensure a thin water supply and self-cleaning capability. The porous polydopamine (PDA) layer on a nickel skeleton provides photothermal functionality and water microchannels, while the thermo-responsive sporopollenin layer on the bottom acts as a switchable water gate. Using confocal laser microscopy and micro-CT, we demonstrate that this unique structure ensures a steady supply of thin water layers, enhancing evaporation by minimizing latent heat at high temperatures. Additionally, the system initiates a self-cleaning process through bulk water convection when temperature drops due to salt accumulation, thus maintaining increased evaporation efficiency. Therefore, the optimized p-SDWE sample achieved a high evaporation rate of 3.58 kg m-2 h-1 using 93.9% solar energy from 1 sun irradiation, and produces 18-22 liters of purified water per square meter of SDWE per day from brine water. This dynamic water transport mechanism surpasses traditional day-night cycles, offering inherent thermal adaptability for continuous, high-efficiency evaporation.

Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast

The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how co-option of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.

Antibacterial activity of Hungarian varietal honeys against respiratory pathogens as a function of storage time

Today, antibiotic therapies that previously worked well against certain bacteria due to their natural sensitivity, are becoming less effective. Honey has been proven to inhibit the biofilm formation of some respiratory bacteria, however few data are available on how the storage time affects the antibacterial effect. The activity of black locust, goldenrod, linden and sunflower honeys from three consecutive years (2020, 2021, 2022) was analyzed in 2022 against Gram-negative (Haemophilus influenzae, H. parainfluenzae, Pseudomonas aeruginosa) and Gram-positive (Streptococcus pneumoniae) bacteria using in vitro microbiological methods. After determining the physicochemical parameters of honey, broth microdilution was applied to determine the minimum inhibitory concentration of each honey type against each bacterium, and crystal violet assay was used to test their antibiofilm effect. The possible mechanism of action was explored with membrane degradation test, while structural changes were illustrated with scanning electron microscopy. Honeys stored for one or two years were darker than fresh honeys, while older honeys had significantly lower antibacterial activity. The most remarkable inhibitory effect was exerted by linden and sunflower honeys, and P. aeruginosa proved to be the most resistant bacterium. Based on our results, honey intended for medicinal purposes should be used as fresh as possible during a treatment.

Plant-derived bioactive compounds for the inhibition of biofilm formation: a comprehensive review

Biofilm formation is a widespread phenomenon that impacts different fields, including the food industry, agriculture, health care and the environment. Accordingly, there is a serious need for new methods of managing the problem of biofilm formation. Natural products have historically been a rich source of varied compounds with a wide variety of biological functions, including antibiofilm agents. In this review, we critically highlight and discuss the recent progress in understanding the antibiofilm effects of several bioactive compounds isolated from different plants, and in elucidating the underlying mechanisms of action and the factors influencing their adhesion. The literature shows that bioactive compounds have promising antibiofilm potential against both Gram-negative and Gram-positive bacterial and fungal strains, via several mechanisms of action, such as suppressing the formation of the polymer matrix, limiting O2 consumption, inhibiting microbial DNA replication, decreasing hydrophobicity of cell surfaces and blocking the quorum sensing network. This antibiofilm activity is influenced by several environmental factors, such as nutritional cues, pH values, O2 availability and temperature. This review demonstrates that several bioactive compounds could mitigate the problem of biofilm production. However, toxicological assessment and pharmacokinetic investigations of these molecules are strongly required to validate their safety.

Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy

The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.

Liposomal drug delivery strategies to eradicate bacterial biofilms: Challenges, recent advances, and future perspectives

Typical antibiotic treatments are often ineffectual against biofilm-related infections since bacteria residing within biofilms have developed various mechanisms to resist antibiotics. To overcome these limitations, antimicrobial-loaded liposomal nanoparticles are a promising anti-biofilm strategy as they have demonstrated improved antibiotic delivery and eradication of bacteria residing in biofilms. Antibiotic-loaded liposomal nanoparticles revealed remarkably higher antibacterial and anti-biofilm activities than free drugs in experimental settings. Moreover, liposomal nanoparticles can be used efficaciously for the combinational delivery of antibiotics and other antimicrobial compounds/peptide which facilitate, for instance, significant breakdown of the biofilm matrix, increased bacterial elimination from biofilms and depletion of metabolic activity of various pathogens. Drug-loaded liposomes have mitigated recurrent infections and are considered a promising tool to address challenges associated to antibiotic resistance. Furthermore, it has been demonstrated that surface charge and polyethylene glycol modification of liposomes have a notable impact on their antibacterial biofilm activity. Future investigations should tackle the persistent hurdles associated with development of safe and effective liposomes for clinical application and investigate novel antibacterial treatments, including CRISPR-Cas gene editing, natural compounds, phages, and nano-mediated approaches. Herein, we emphasize the significance of liposomes in inhibition and eradication of various bacterial biofilms, their challenges, recent advances, and future perspectives.

Dissecting cell heterogeneities in bacterial biofilms and their implications for antibiotic tolerance

Bacterial biofilms consist of large, self-formed aggregates where resident bacteria can exhibit very different physiological states and phenotypes. This heterogeneity of cell types is crucial for many structural and functional emergent properties of biofilms. Consequently, it becomes essential to understand what drives cells to differentiate and how they achieve it within the three-dimensional landscape of the biofilms. Here, we discuss recent advances in comprehending two forms of cell heterogeneity that, while recognized to coexist within biofilms, have proven challenging to distinguish. These two forms include cell heterogeneity arising as a consequence of bacteria physiologically responding to resource gradients formed across the biofilms and cell-to-cell phenotypic heterogeneity, which emerges locally within biofilm subzones among neighboring bacteria due to stochastic variations in gene expression. We describe the defining features and concepts related to both forms of cell heterogeneity and discuss their implications, with a particular focus on antibiotic tolerance.

Nano-Bio Interactions: Biofilm-Targeted Antibacterial Nanomaterials

Biofilm is a spatially organized community formed by the accumulation of both microorganisms and their secretions, leading to persistent and chronic infections because of high resistance toward conventional antibiotics. In view of the tunable physicochemical properties and the related unique biological behavior (e.g., size-, shape-, and surface charge-dependent penetration, protein corona endowed targeting, catalytic- and electronic-related oxidative stress, optical- and magnetic-associated hyperthermia, etc.), nanomaterials-based therapeutics are widely used for the treatment of biofilm-associated infections. In this review, the biological characteristics of biofilm are introduced. And the nanomaterials-based antibacterial strategies are further discussed via biofilm targeting, including preventing biofilm formation, enhancing biofilm penetration, disrupting the mature biofilm, and acting as drug delivery systems. In which, the interactions between biofilm and nanomaterials include mechanical disruption, electron transfer, enzymatic degradation, oxidative stress, and hyperthermia. Additionally, the current advances of nanomaterials for antibacterial nanomaterials by biofilm targeting are summarized. This review aims to present a complete vision of antibacterial nanomaterials-biofilm (nano-bio) interactions, paving the way for the future development and clinical translation of effective antibacterial nanomedicines.

Cellular arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms

Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.

The motility-matrix production switch in Bacillus subtilis-a modeling perspective

Phenotype switching can be triggered by external stimuli and by intrinsic stochasticity. Here, we focus on the motility-matrix production switch in Bacillus subtilis. We use modeling to describe the SinR-SlrR bistable switch and its regulation by SinI and to distinguish different sources of stochasticity. Our simulations indicate that intrinsic fluctuations in the synthesis of SinI are insufficient to drive spontaneous switching and suggest that switching is triggered by upstream noise from the Spo0A phosphorelay. IMPORTANCE The switch from motility to matrix production is the first step toward biofilm formation and, thus, to multicellular behavior in Bacillus subtilis. The transition is governed by a bistable switch based on the interplay of the regulators SinR and SlrR, while SinI transmits upstream signals to that switch. Quantitative modeling can be used to study the switching dynamics. Here, we build such a model step by step to describe the dynamics of the switch and its regulation and to study how spontaneous switching is triggered by upstream noise from the Spo0A phosphorelay.

Multiscale spatial segregation analysis in digital images of biofilms

Quantifying the degree of spatial segregation of two bacterial strains in mixed biofilms is an important topic in microbiology. Spatial segregation is dependent on spatial scale as two strains may appear to be well mixed if observed from a distance, but a closer look can reveal strong separation. Typically, this information is encoded in a digital image that represents the binary system, e.g., a microscopy image of a two species biofilm. To decode spatial segregation information, we have developed quantitative measures for evaluating the degree of the spatial scale-dependent segregation of two bacterial strains in a digital image. The constructed algorithm is based on the new segregation measures and overcomes drawbacks of existing approaches for biofilm segregation analysis. The new approach is implemented in a freely available software and was successfully applied to biofilms of two strains and bacterial suspensions for detection of the different spatial scale-dependent segregation levels.

Bacillus subtilis NDmed, a model strain for biofilm genetic studies

The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.

Human Induced Pluripotent Spheroids' Growth Is Driven by Viscoelastic Properties and Macrostructure of 3D Hydrogel Environment

Stem cells, particularly human iPSCs, constitute a powerful tool for tissue engineering, notably through spheroid and organoid models. While the sensitivity of stem cells to the viscoelastic properties of their direct microenvironment is well-described, stem cell differentiation still relies on biochemical factors. Our aim is to investigate the role of the viscoelastic properties of hiPSC spheroids' direct environment on their fate. To ensure that cell growth is driven only by mechanical interaction, bioprintable alginate-gelatin hydrogels with significantly different viscoelastic properties were utilized in differentiation factor-free culture medium. Alginate-gelatin hydrogels of varying concentrations were developed to provide 3D environments of significantly different mechanical properties, ranging from 1 to 100 kPa, while allowing printability. hiPSC spheroids from two different cell lines were prepared by aggregation (⌀ = 100 µm, n > 1 × 104), included and cultured in the different hydrogels for 14 days. While spheroids within dense hydrogels exhibited limited growth, irrespective of formulation, porous hydrogels prepared with a liquid-liquid emulsion method displayed significant variations of spheroid morphology and growth as a function of hydrogel mechanical properties. Transversal culture (adjacent spheroids-laden alginate-gelatin hydrogels) clearly confirmed the separate effect of each hydrogel environment on hiPSC spheroid behavior. This study is the first to demonstrate that a mechanically modulated microenvironment induces diverse hiPSC spheroid behavior without the influence of other factors. It allows one to envision the combination of multiple formulations to create a complex object, where the fate of hiPSCs will be independently controlled by their direct microenvironment.

Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities

Bacillus subtilis can form various types of spatially organised communities on surfaces, such as colonies, pellicles and submerged biofilms. These communities share similarities and differences, and phenotypic heterogeneity has been reported for each type of community. Here, we studied spatial transcriptional heterogeneity across the three types of surface-associated communities. Using RNA-seq analysis of different regions or populations for each community type, we identified genes that are specifically expressed within each selected population. We constructed fluorescent transcriptional fusions for 17 of these genes, and observed their expression in submerged biofilms using time-lapse confocal laser scanning microscopy (CLSM). We found mosaic expression patterns for some genes; in particular, we observed spatially segregated cells displaying opposite regulation of carbon metabolism genes (gapA and gapB), indicative of distinct glycolytic or gluconeogenic regimes coexisting in the same biofilm region. Overall, our study provides a direct comparison of spatial transcriptional heterogeneity, at different scales, for the three main models of B. subtilis surface-associated communities.

Comparative Study of Quercetin and Hyperoside: Antimicrobial Potential towards Food Spoilage Bacteria, Mode of Action and Molecular Docking

The antibacterial activities of quercetin and hyperoside were evaluated towards two major spoilage bacteria in fish, Pseudomonas aeruginosa (PA) and Shewanella putrefaciens (SP). Hyperoside showed a lower minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) towards both spoilage bacteria, PA and SP, than quercetin. Cell membrane morphology was affected when treated with hyperoside and quercetin. The release of content from the treated cells occurred, as ascertained by the release of potassium and magnesium ions and the increase in conductivity of the culture media. The morphology of cells was significantly changed, in which shrinkage and pores were obtained, when observed using SEM. Both compounds negatively affected the motility, both swimming and swarming, and the formation of extracellular polymeric substance (EPS), thus confirming antibiofilm activities. Agarose gel analysis revealed that both compounds could bind to or degrade the genomic DNA of both bacteria, thereby causing bacterial death. Molecular docking indicated that the compounds interacted with the minor groove of the DNA, favoring the adenine-thymine-rich regions. Thus, both quercetin and hyperoside could serve as potential antimicrobial agents to retard the spoilage of fish or perishable products.

Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms

Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.

Matrix Producing Cells Induce the Morphological Difference in the Bacillus subtilis Biofilm

There is a 'coffee ring' in the Bacillus subtilis biofilm center, and the colony biofilm morphologies are distinct inside and outside the 'coffee ring'. In this paper, we study this morphological difference and explain the reasons of the 'coffee ring' formation and further the causes to the morphological variation. We developed a quantitative method to characterize the surface morphology, the outer area is thicker than the inner area of the 'coffee ring', and the thickness amplitude in outer area is larger than inner area of the 'coffee ring'. We adopt a logistic growth model to obtain how the environmental resistance influence the colony biofilm thickness. Dead cells provide gaps for stress release and make folds formation in colony biofilm. we developed a technique for optical imaging and matching cells with the BRISK algorithm to capture the distribution and movement of motile cells and matrix producing cells in the colony biofilm. Matrix producing cells are mainly distribute in the outside of the 'coffee ring', and the extracellular matrix (ECM) prevents the motile cells moving outward from center. Motile cells mainly locate inside the ring, a small amount of dead motile cells outside the 'coffee ring' give rise to radial folds formation. There are no ECM blocking cell movements inside the ring, which result in uniform folds formation. The distribution of ECM and different phenotypes lead to the formation of the 'coffee ring', which is verified by using eps and flagellar mutants.

Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media

Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.

Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics

The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a quasi-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.

Vertical growth dynamics of biofilms

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing these models, or their biophysical underpinnings, empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of vertical growth dynamics. We propose a heuristic model for vertical growth dynamics based on basic biophysical processes inside a biofilm: diffusion and consumption of nutrients and growth and decay of the colony. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi.

Altering the viscoelastic properties of mucus-grown Pseudomonas aeruginosa biofilms affects antibiotic susceptibility

The viscoelastic properties of biofilms are correlated with their susceptibility to mechanical and chemical stress, and the airway environment in muco-obstructive pulmonary diseases (MOPD) facilitates robust biofilm formation. Hyperconcentrated, viscoelastic mucus promotes chronic inflammation and infection, resulting in increased mucin and DNA concentrations. The viscoelastic properties of biofilms are regulated by biopolymers, including polysaccharides and DNA, and influence responses to antibiotics and phagocytosis. We hypothesize that targeted modulation of biofilm rheology will compromise structural integrity and increase antibiotic susceptibility and mucociliary transport. We evaluate biofilm rheology on the macro, micro, and nano scale as a function of treatment with a reducing agent, a biopolymer, and/or tobramycin to define the relationship between the viscoelastic properties of biofilms and susceptibility. Disruption of the biofilm architecture is associated with altered macroscopic and microscopic moduli, rapid vector permeability, increased antibiotic susceptibility, and improved mucociliary transport, suggesting that biofilm modulating therapeutics will improve the treatment of chronic respiratory infections in MOPD.

Drug delivery approaches for enhanced antibiofilm therapy

Biofilms have attracted increasing attention in recent years. Many bacterial infections are associated with biofilm formation. A bacterial biofilm is an aggregated membrane-like substance that is composed of a large number of bacteria and their secreted extracellular polymeric substances. The traditional antibiofilm approaches, such as chemotherapy based on antibiotics, are often ineffective in eradicating biofilms owing to the limited diffusion ability of antibiotics within biofilms and inactivation of antibiotics by biofilms. Moreover, a larger dosage of antibiotics could be effective, but leads to an increased tolerance. Smart drug delivery systems that deliver antibiotics into the biofilm interior is a promising strategy to meet this challenge. In this review, we focus on the methods to improve drug delivery efficiency for enhanced chemotherapy of biofilms. Furthermore, we have summarized chemical approaches for enhanced drug delivery, such as chemical shields, charge reversal, and dual corona enhanced delivery strategies; these methods focus on physicochemical biofilm properties and specific biofilm features. Afterwards, physical approaches are discussed, such as magnetism-mediated drug delivery, electricity-mediated drug delivery, ultrasound-mediated drug delivery, and shock wave-mediated drug delivery. Finally, a perspective on the development of next-generation antibiofilm drug delivery systems is given.

The role of biofilm matrix composition in controlling colony expansion and morphology

Biofilms are biological viscoelastic gels composed of bacterial cells embedded in a self-secreted polymeric extracellular matrix (ECM). In environmental settings, such as in the rhizosphere and phyllosphere, biofilm colonization occurs at the solid-air interface. The biofilms' ability to colonize and expand over these surfaces depends on the formation of osmotic gradients and ECM viscoelastic properties. In this work, we study the influence of biofilm ECM components on its viscoelasticity and expansion, using the model organism Bacillus subtilis and deletion mutants of its three major ECM components, TasA, EPS and BslA. Using a multi-scale approach, we quantified macro-scale viscoelasticity and expansion dynamics. Furthermore, we used a microsphere assay to visualize the micro-scale expansion patterns. We find that the viscoelastic phase angle Φ is likely the best viscoelastic parameter correlating to biofilm expansion dynamics. Moreover, we quantify the sensitivity of the biofilm to changes in substrate water potential as a function of ECM composition. Finally, we find that the deletion of ECM components significantly increases the coherence of micro-scale colony expansion patterns. These results demonstrate the influence of ECM viscoelasticity and substrate water potential on the expansion of biofilm colonies on wet surfaces at the air-solid interface, commonly found in natural environments.

'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms

Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis

Many bacterial species typically live in complex three-dimensional biofilms, yet much remains unknown about differences in essential processes between nonbiofilm and biofilm lifestyles. Here, we created a CRISPR interference (CRISPRi) library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain NCIB 3610 and investigated growth, biofilm colony wrinkling, and sporulation phenotypes of the knockdown library. First, we showed that gene essentiality is largely conserved between liquid and surface growth and between two media. Second, we quantified biofilm colony wrinkling using a custom image analysis algorithm and found that fatty acid synthesis and DNA gyrase knockdown strains exhibited increased wrinkling independent of biofilm matrix gene expression. Third, we designed a high-throughput screen to quantify sporulation efficiency after essential gene knockdown; we found that partial knockdowns of essential genes remained competent for sporulation in a sporulation-inducing medium, but knockdown of essential genes involved in fatty acid synthesis exhibited reduced sporulation efficiency in LB, a medium with generally lower levels of sporulation. We conclude that a subset of essential genes are particularly important for biofilm structure and sporulation/germination and suggest a previously unappreciated and multifaceted role for fatty acid synthesis in bacterial lifestyles and developmental processes. IMPORTANCE For many bacteria, life typically involves growth in dense, three-dimensional communities called biofilms that contain cells with differentiated roles held together by extracellular matrix. To examine how essential gene function varies between vegetative growth and the developmental states of biofilm formation and sporulation, we created and screened a comprehensive library of strains using CRISPRi to knockdown expression of each essential gene in the biofilm-capable Bacillus subtilis strain 3610. High-throughput assays and computational algorithms identified a subset of essential genes involved in biofilm wrinkling and sporulation and indicated that fatty acid synthesis plays important and multifaceted roles in bacterial development.

Advancements in antimicrobial nanoscale materials and self-assembling systems

Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.

An open-source computational tool for measuring bacterial biofilm morphology and growth kinetics upon one-sided exposure to an antimicrobial source

Bacillus subtilis biofilms are well known for their complex and highly adaptive morphology. Indeed, their phenotypical diversity and intra-biofilm heterogeneity make this gram-positive bacterium the subject of many scientific papers on the structure of biofilms. The “robustness” of biofilms is a term often used to describe their level of susceptibility to antimicrobial agents and various mechanical and molecular inhibition/eradication methods. In this paper, we use computational analytics to quantify Bacillus subtilis morphological response to proximity to an antimicrobial source, in the form of the antiseptic chlorhexidine. Chlorhexidine droplets, placed in proximity to Bacillus subtilis macrocolonies at different distances result in morphological changes, quantified using Python-based code, which we have made publicly available. Our results quantify peripheral and inner core deformation as well as differences in cellular viability of the two regions. The results reveal that the inner core, which is often characterized by the presence of wrinkled formations in the macrocolony, is more preserved than the periphery. Furthermore, the paper describes a crescent-shaped colony morphology which occurs when the distance from the chlorhexidine source is 0.5 cm, as well as changes observed in the growth substrate of macrocolonies exposed to chlorhexidine.

The Role of Staphylococcal Biofilm on the Surface of Implants in Orthopedic Infection

Despite advanced implant sterilization and aseptic surgical techniques, implant-associated infection remains a major challenge for orthopedic surgeries. The subject of bacterial biofilms is receiving increasing attention, probably as a result of the wide acknowledgement of the ubiquity of biofilms in the clinical environment, as well as the extreme difficulty in eradicating them. Biofilm can be defined as a structured microbial community of cells that are attached to a substratum and embedded in a matrix of extracellular polymeric substances (EPS) that they have produced. Biofilm development has been proposed as occurring in a multi-step process: (i) attachment and adherence, (ii) accumulation/maturation due to cellular aggregation and EPS production, and (iii) biofilm detachment (also called dispersal) of bacterial cells. In all these stages, characteristic proteinaceous and non-proteinaceous compounds are expressed, and their expression is strictly controlled. Bacterial biofilm formation around implants shelters the bacteria and encourages the persistence of infection, which could lead to implant failure and osteomyelitis. These complications need to be treated by major revision surgeries and extended antibiotic therapies, which could lead to high treatment costs and even increase mortality. Effective preventive and therapeutic measures to reduce risks for implant-associated infections are thus in urgent need.

Fungicidal and antibiofilm activities of gold nanoparticles on Candida tropicalis

Aim: To investigate the antifungal activity of two different functionalized gold nanoparticles (AuNP), those stabilized with cetyltrimethylammonium bromide and those conjugated with cysteine, and their effects on the architecture of Candida tropicalis biofilms. Materials & methods: Biofilms were studied by crystal violet binding assay and scanning electron microscopy. We investigated the effects of AuNPs on reactive oxygen species, reactive nitrogen intermediates and enzymatic and nonenzymatic antioxidant defenses. Results/Conclusion: The fungicidal activity and cellular stress of both AuNPs affected biofilm growth through accumulation of reactive oxygen species and reactive nitrogen intermediates. However, cetyltrimethylammonium bromide-stabilized AuNPs revealed a higher redox imbalance. We correlated, for the first time, AuNP effects with the redox imbalance and alterations in the architecture of C. tropicalis biofilms.

Bactericidal Efficacy of Oxidized Silver against Biofilms Formed by Curtobacterium flaccumfaciens pv. flaccumfaciens

Bacterial wilt is a re-emerging disease on dry bean and can affect many other crop species within the Fabaceae. The causal agent, Curtobacterium flaccumfaciens pv. flaccumfaciens (CFF), is a small, Gram-positive, rodshaped bacterium that is seed-transmitted. Infections in the host become systemic, leading to wilting and economic loss. Clean seed programs and bactericidal seed treatments are two critical management tools. This study characterizes the efficacies of five bactericidal chemicals against CFF. It was hypothesized that this bacterium was capable of forming biofilms, and that the cells within biofilms would be more tolerant to bactericidal treatments. The minimum biocide eradication concentration assay protocol was used to grow CFF biofilms, expose the biofilms to bactericides, and enumerate survivors compared to a non-treated control (water). Streptomycin and oxysilver bisulfate had EC95 values at the lowest concentrations and are likely the best candidates for seed treatment products for controlling seed-borne bacterial wilt of bean. The results showed that CFF formed biofilms during at least two phases of the bacterial wilt disease cycle, and the biofilms were much more difficult to eradicate than their planktonic counterparts. Overall, biofilm formation by CFF is an important part of the bacterial wilt disease cycle in dry edible bean and antibiofilm bactericides such as streptomycin and oxysilver bisulfate may be best suited for use in disease management.

Fractal morphology facilitates Bacillus subtilis biofilm growth

In the late stage of Bacillus subtilis biofilm growth, to adapt the extremely nutrient-lacking environment, the biofilm edge grows into a complex branching structure, which allows the biofilm to expand outward at a faster speed, comparing to the expansion speed of the biofilm edge without branching structure. The fractal analysis shows that the fractal dimension (Fd) decreases along the radius in the biofilm branching structure, as shown in Figs. 1d and 3a. The variation of Fd along the radius is not monotonic, which is because of the texture evolution induced by the bacterial clusters' movement. By using the wide field stereomicroscope and image analysis, we find that the ridges in the mature branching structure are composed of inactive substances, and most of the bacterial clusters move through the valleys. Further analysis shows that bacterial clusters move to the area with the high Succolarity (Suc) value.

Competition between growth and shear stress drives intermittency in preferential flow paths in porous medium biofilms

Bacteria in porous media, such as soils, aquifers, and filters, often form surface-attached communities known as biofilms. Biofilms are affected by fluid flow through the porous medium, for example, for nutrient supply, and they, in turn, affect the flow. A striking example of this interplay is the strong intermittency in flow that can occur when biofilms nearly clog the porous medium. Intermittency manifests itself as the rapid opening and slow closing of individual preferential flow paths (PFPs) through the biofilm-porous medium structure, leading to continual spatiotemporal rearrangement. The drastic changes to the flow and mass transport induced by intermittency can affect the functioning and efficiency of natural and industrial systems. Yet, the mechanistic origin of intermittency remains unexplained. Here, we show that the mechanism driving PFP intermittency is the competition between microbial growth and shear stress. We combined microfluidic experiments quantifying Bacillus subtilis biofilm formation and behavior in synthetic porous media for different pore sizes and flow rates with a mathematical model accounting for flow through the biofilm and biofilm poroelasticity to reveal the underlying mechanisms. We show that the closing of PFPs is driven by microbial growth, controlled by nutrient mass flow. Opposing this, we find that the opening of PFPs is driven by flow-induced shear stress, which increases as a PFP becomes narrower due to microbial growth, causing biofilm compression and rupture. Our results demonstrate that microbial growth and its competition with shear stresses can lead to strong temporal variability in flow and transport conditions in bioclogged porous media.

Electrospun Nanofibrous Membranes Accelerate Biofilm Formation and Probiotic Enrichment: Enhanced Tolerances to pH and Antibiotics

Biofilms are the oldest, most successful, and most widely distributed form of microorganism life on earth, existing even in extreme environments. Presently, probiotics in biofilm phenotype are thought as the most advanced fourth-generation probiotics. However, high-efficiency and large-scale biofilm enrichment in an artificial way is difficult. Here, fibrous membranes as probiotic biofilm-enriching materials are studied. Electrospun cellulose acetate nanofibrous membranes with nano-sized fibers show outstanding superiority over fibrous membranes with micron-sized fibers in Lactobacillus paracasei biofilm enrichment. The special 3D structure of electrospun nanofibrous membranes makes other facilitating biofilm formation factors insignificant. With a suitable scaffold/culture medium ratio, nearly 100% of L. paracasei cells exist as biofilm phenotype on the membrane from the very beginning, not planktonic state. L. paracasei biofilms possess a potential for long-term survival and high tolerances toward strong acidic and alkali conditions and antibiotics. RNA sequencing results explain why L. paracasei biofilms possess high tolerances toward harsh environments as compared to planktonic L. paracasei. Electrospun nanofibrous membranes can serve as powerful biofilm-enriching scaffolds for probiotics and other valuable microbes.

A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics

Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities.

IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.

Engineered Living Hydrogels

Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.

The role of surface adhesion on the macroscopic wrinkling of biofilms

Biofilms, bacterial communities of cells encased by a self-produced matrix, exhibit a variety of three-dimensional structures. Specifically, channel networks formed within the bulk of the biofilm have been identified to play an important role in the colonies' viability by promoting the transport of nutrients and chemicals. Here, we study channel formation and focus on the role of the adhesion of the biofilm matrix to the substrate in Pseudomonas aeruginosa biofilms grown under constant flow in microfluidic channels. We perform phase contrast and confocal laser scanning microscopy to examine the development of the biofilm structure as a function of the substrates' surface energy. The formation of the wrinkles and folds is triggered by a mechanical buckling instability, controlled by biofilm growth rate and the film’s adhesion to the substrate. The three-dimensional folding gives rise to hollow channels that rapidly increase the effective volume occupied by the biofilm and facilitate bacterial movement inside them. The experiments and analysis on mechanical instabilities for the relevant case of a bacterial biofilm grown during flow enable us to predict and control the biofilm morphology.

The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms

In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.

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The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms

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A novel subpopulation—mineral-forming cells—is essential for biofilm formation

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This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate

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Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure

Environmental and Biological Controls on Sedimentary Bottom Types in the Puquios of the Salar de Llamara, Northern Chile

The Puquios of the Salar de Llamara in the Atacama Desert, northern Chile, is a system of small lakes that is characterized by evaporitic mineral deposition and that commonly hosts microbial communities. This region is known for its extreme aridity, solar irradiance, and temperature fluctuations. The Puquios are a highly diverse ecosystem with a variety of sedimentary bottom types. Our previous results identified electrical conductivity (EC) as a first-order environmental control on bottom types. In the present paper, we extend our analysis to examine the effects of additional environmental parameters on bottom types and to consider reasons for the importance of EC as a control of sedimentology. Our results identify microbially produced extracellular polymeric substances (EPS) as a major player in the determination of bottom types. The relative amounts and properties of EPS are determined by EC. EPS, in turn, determines the consistency of bottom types, exchange of bottom substrate with the overlying water column, and mineral precipitation within the substrate. Low-EC ponds in the Puquios system have flocculent to semi-cohesive bottom types, with low-viscosity EPS that allows for high-exchange with the surrounding waters and mineral precipitation of granular gypsum, carbonate, and Mg–Si clay in close association with microbes. Ponds with elevated EC have bottom types that are laminated and highly cohesive with high-viscosity EPS that restricts the exchange between sediments and the surrounding waters; mineral precipitation in these high-EC ponds includes granular to laminated gypsum, carbonate and Mg–Si, which also form in close association with microbes. Bottom types in ponds with EC above the threshold for thriving benthic microbial communities have insufficient EPS accumulations to affect mineral precipitation, and the dominant mineral is gypsum (selenite). The variations in EPS production throughout the Puquios, associated with heterogeneity in environmental conditions, make the Puquios region an ideal location for understanding the controls of sedimentary bottom types in evaporative extreme environments that may be similar to those that existed on early Earth and beyond.

Groovy and Gnarly: Surface Wrinkles as a Multifunctional Motif for Terrestrial and Marine Environments

From large ventral pleats of humpback whales to nanoscale ridges on flower petals, wrinkled structures are omnipresent, multifunctional, and found at hugely diverse scales. Depending on the particulars of the biological system-its environment, morphology, and mechanical properties-wrinkles may control adhesion, friction, wetting, or drag; promote interfacial exchange; act as flow channels; or contribute to stretching, mechanical integrity, or structural color. Undulations on natural surfaces primarily arise from stress-induced instabilities of surface layers (e.g., buckling) during growth or aging. Variation in the material properties of surface layers and in the magnitude and orientation of intrinsic stresses during growth lead to a variety of wrinkling morphologies and patterns which, in turn, reflect the wide range of biophysical challenges wrinkled surfaces can solve. Therefore, investigating how surface wrinkles vary and are implemented across biological systems is key to understanding their structure-function relationships. In this work, we synthesize the literature in a metadata analysis of surface wrinkling in various terrestrial and marine organisms to review important morphological parameters and classify functional aspects of surface wrinkles in relation to the size and ecology of organisms. Building on our previous and current experimental studies, we explore case studies on nano/micro-scale wrinkles in biofilms, plant surfaces, and basking shark filter structures to compare developmental and structure-vs-function aspects of wrinkles with vastly different size scales and environmental demands. In doing this and by contrasting wrinkle development in soft and hard biological systems, we provide a template of structure-function relationships of biological surface wrinkles and an outlook for functionalized wrinkled biomimetic surfaces.

Varied solutions to multicellularity: The biophysical and evolutionary consequences of diverse intercellular bonds

The diversity of multicellular organisms is, in large part, due to the fact that multicellularity has independently evolved many times. Nonetheless, multicellular organisms all share a universal biophysical trait: cells are attached to each other. All mechanisms of cellular attachment belong to one of two broad classes; intercellular bonds are either reformable or they are not. Both classes of multicellular assembly are common in nature, having independently evolved dozens of times. In this review, we detail these varied mechanisms as they exist in multicellular organisms. We also discuss the evolutionary implications of different intercellular attachment mechanisms on nascent multicellular organisms. The type of intercellular bond present during early steps in the transition to multicellularity constrains future evolutionary and biophysical dynamics for the lineage, affecting the origin of multicellular life cycles, cell-cell communication, cellular differentiation, and multicellular morphogenesis. The types of intercellular bonds used by multicellular organisms may thus result in some of the most impactful historical constraints on the evolution of multicellularity.

A Journey into Animal Models of Human Osteomyelitis: A Review

Osteomyelitis is an infection of the bone characterized by progressive inflammatory destruction and apposition of new bone that can spread via the hematogenous route (hematogenous osteomyelitis (HO)), contiguous spread (contiguous osteomyelitis (CO)), and direct inoculation (osteomyelitis associated with peripheral vascular insufficiency (PVI)). Given the significant financial burden posed by osteomyelitis patient management, the development of new preventive and treatment methods is warranted. To achieve this objective, implementing animal models (AMs) of infection such as rats, mice, rabbits, avians, dogs, sheep, goats, and pigs might be of the essence. This review provides a literature analysis of the AMs developed and used to study osteomyelitis. Historical relevance and clinical applicability were taken into account to choose the best AMs, and some study methods are briefly described. Furthermore, the most significant strengths and limitations of each species as AM are discussed, as no single model incorporates all features of osteomyelitis. HO’s clinical manifestation results in extreme variability between patients due to multiple variables (e.g., age, sex, route of infection, anatomical location, and concomitant diseases) that could alter clinical studies. However, these variables can be controlled and tested through different animal models.

Nanocarriers for combating biofilms: advantages and challenges

Bacterial biofilms are highly resistant to antibiotics and pose a great threat to human and animal health. The control and removal of bacterial biofilms have become an important topic in the field of bacterial infectious diseases. Nanocarriers show great anti-biofilm potential because of their small particle size and strong permeability. In this review, the advantages of nanocarriers for combating biofilms are analyzed. Nanocarriers can act on all stages of bacterial biofilm formation and diffusion. They can improve the scavenging effect of biofilm by targeting biofilm, destroying extracellular polymeric substances, and enhancing the biofilm permeability of antimicrobial substances. Nanocarriers can also improve the antibacterial ability of antimicrobial drugs against bacteria in biofilm by protecting the loaded drugs and controlling the release of antimicrobial substances. Additionally, we emphasize the challenges faced in using nanocarrier formulations and translating them from a preclinical level to the clinical setting.

Materials science and mechanosensitivity of living matter

Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The challenge is that biomaterials often exist far from equilibrium, either in a kinetically arrested state or in an energy consuming active state that is not yet possible to reproduce de novo. Also, the design principles that form biological materials often result in nonlinear responses of stress to strain, or force to displacement, and theoretical models to explain these nonlinear effects are in relatively early stages of development compared to the predictive models for rubberlike elastomers or metals. In this Review, we summarize some of the most common and striking mechanical features of biological materials and make comparisons among animal, plant, fungal, and bacterial systems. We also summarize some of the mechanisms by which living systems develop forces that shape biological matter and examine newly discovered mechanisms by which cells sense and respond to the forces they generate themselves, which are resisted by their environment, or that are exerted upon them by their environment. Within this framework, we discuss examples of how physical methods are being applied to cell biology and bioengineering.

Antibacterial effect of bacteriocin XJS01 and its application as antibiofilm agents to treat multidrug-resistant Staphylococcus aureus infection

Multidrug-resistant (MDR) Staphylococcus aureus biofilms have emerged as a serious threat to human health. Recently, the development of antibiotic replacement therapy has gained much attention due to the potential application of bacteriocin. The present study sought to evaluate the antibacterial effect of bacteriocin XJS01 against MDR S. aureus, a previously reported bacteriocin against S. aureus strain 2612:1606BL1486 (S. aureus_26, an MDR strain demonstrated here), and its potential application as an antibiofilm agent. The minimum bactericide concentration of XJS01 against MDR S. aureus_26 was 33.18 μg/mL. XJS01 exhibited excellent storage stability and resistance against acid and reduced the density of established MDR S. aureus_26 biofilm. The hemolytic and HEK293T cytotoxicity activities of XJS01 and the histological analyses in mice confirmed its safety. Moreover, XJS01 effectively disrupted the MDR S. aureus_26 biofilm established on the skin wound surface and reduced the biofilm-isolated bacteria, thereby decreasing the release of pro-inflammatory cytokines and the proliferation of alternatively activated macrophages. Compared to mupirocin, XJS01 exhibited an excellent therapeutic effect on mice skin wounds, confirming it to be a potential alternative to antibiotics.

Multiscale X-ray study of Bacillus subtilis biofilms reveals interlinked structural hierarchy and elemental heterogeneity

Biofilms are multicellular, soft microbial communities that are able to colonize synthetic surfaces as well as living organisms. To survive sudden environmental changes and efficiently share their common resources, cells in a biofilm divide into subgroups with distinct functions, leading to phenotypic heterogeneity. Here, by studying intact biofilms by synchrotron X-ray diffraction and fluorescence, we revealed correlations between biofilm macroscopic, architectural heterogeneity and the spatiotemporal distribution of extracellular matrix, spores, water, and metal ions. Our findings demonstrate that biofilm heterogeneity is not only affected by local genetic expression and cellular differentiation but also by passive effects resulting from the physicochemical properties of the molecules secreted by the cells, leading to differential distribution of nutrients that propagate through macroscopic length scales.

Biofilms are multicellular microbial communities that encase themselves in an extracellular matrix (ECM) of secreted biopolymers and attach to surfaces and interfaces. Bacterial biofilms are detrimental in hospital and industrial settings, but they can be beneficial, for example, in agricultural as well as in food technology contexts. An essential property of biofilms that grants them with increased survival relative to planktonic cells is phenotypic heterogeneity, the division of the biofilm population into functionally distinct subgroups of cells. Phenotypic heterogeneity in biofilms can be traced to the cellular level; however, the molecular structures and elemental distribution across whole biofilms, as well as possible linkages between them, remain unexplored. Mapping X-ray diffraction across intact biofilms in time and space, we revealed the dominant structural features in Bacillus subtilis biofilms, stemming from matrix components, spores, and water. By simultaneously following the X-ray fluorescence signal of biofilms and isolated matrix components, we discovered that the ECM preferentially binds calcium ions over other metal ions, specifically, zinc, manganese, and iron. These ions, remaining free to flow below macroscopic wrinkles that act as water channels, eventually accumulate and may possibly lead to sporulation. The possible link between ECM properties, regulation of metal ion distribution, and sporulation across whole, intact biofilms unravels the importance of molecular-level heterogeneity in shaping biofilm physiology and development.

Imaging flow cytometry reveals a dual role for exopolysaccharides in biofilms: To promote self-adhesion while repelling non-self-community members

In nature, bacteria frequently reside in differentiated communities or biofilms. These multicellular communities are held together by self-produced polymers that allow the community members to adhere to the surface as well as to neighbor bacteria. Here, we report that exopolysaccharides prevent Bacillus subtilis from co-aggregating with a distantly related bacterium Bacillus mycoides, while maintaining their role in promoting self-adhesion and co-adhesion with phylogenetically related bacterium, Bacillus atrophaeus. The defensive role of the exopolysaccharides is due to the specific regulation of bacillaene. Single cell analysis of biofilm and free-living bacterial cells using imaging flow cytometry confirmed a specific role for the exopolysaccharides in microbial competition repelling B. mycoides. Unlike exopolysaccharides, the matrix protein TasA induced bacillaene but inhibited the expression of the biosynthetic clusters for surfactin, and therefore its overall effect on microbial competition during floating biofilm formation was neutral. Thus, the exopolysaccharides provide a dual fitness advantage for biofilm-forming cells, as it acts to promote co-aggregation of related species, as well as, a secreted cue for chemical interference with non-compatible partners. These results experimentally demonstrate a general assembly principle of complex communities and provides an appealing explanation for how closely related species are favored during community assembly. Furthermore, the differential regulation of surfactin and bacillaene by the extracellular matrix may explain the spatio-temporal gradients of antibiotic production within biofilms.

On-demand pulling-off of magnetic nanoparticles from biomaterial surfaces through implant-associated infectious biofilms for enhanced antibiotic efficacy

Biomaterial-associated infections can occur any time after surgical implantation of biomaterial implants and limit their success rates. On-demand, antimicrobial release coatings have been designed, but in vivo release triggers uniquely relating with infection do not exist, while inadvertent leakage of antimicrobials can cause exhaustion of a coating prior to need. Here, we attach magnetic-nanoparticles to a biomaterial surface, that can be pulled-off in a magnetic field through an adhering, infectious biofilm. Magnetic-nanoparticles remained stably attached to a surface upon exposure to PBS for at least 50 days, did not promote bacterial adhesion or negatively affect interaction with adhering tissue cells. Nanoparticles could be magnetically pulled-off from a surface through an adhering biofilm, creating artificial water channels in the biofilm. At a magnetic-nanoparticle coating concentration of 0.64 mg cm^-2, these by-pass channels increased the penetrability of Staphylococcus aureus and Pseudomonas aeruginosa biofilms towards different antibiotics, yielding 10-fold more antibiotic killing of biofilm inhabitants than in absence of artificial channels. This innovative use of magnetic-nanoparticles for the eradication of biomaterial-associated infections requires no precise targeting of magnetic-nanoparticles and allows more effective use of existing antibiotics by breaking the penetration barrier of an infectious biofilm adhering to a biomaterial implant surface on-demand.