Self-induced mechanical stress can trigger biofilm formation in uropathogenic Escherichia coli

Virulence-linked adhesin drives mutualist colonization of the bee gut via biofilm formation

Bacterial biofilms are stable multicellular structures that can enable long term host association. Yet, the role of biofilms in supporting gut mutualism is still not fully understood. Here, we investigate Snodgrassella alvi, a beneficial bacterial symbiont of honey bees, and find that biofilm formation is required for its colonization of the bee gut. We constructed fifteen S. alvi mutants containing knockouts of genes known to promote colonization with putative roles in biofilm formation. Genes required for colonization included staA and staB, encoding trimeric autotransporter adhesins (TAAs) and mltA, encoding a lytic transglycosylase. Intriguingly, TAAs are considered virulence factors in pathogens but support mutualism by the symbiont S. alvi. In vitro, biofilm formation was reduced in ΔstaB cells and abolished in the other two mutants. Loss of staA also reduced auto-aggregation and cell-cell connections. Based on structural predictions, StaA/B are massive (>300 nm) TAAs with many repeats in their stalk regions. Further, we find that StaA/B are conserved across Snodgrassella species, suggesting that StaA/B-dependent colonization is characteristic of this symbiont lineage. Finally, staA deletion increases sensitivity to bactericidal antimicrobials, suggesting that the biofilm indirectly buffers against antibiotic stress. In all, the inability of two biofilm-deficient strains (ΔstaA and ΔmltA) to effectively mono-colonize bees indicates that S. alvi biofilm formation is required for colonization of the bee gut. We envision the bee gut system as a genetically tractable model for studying the physical basis of biofilm-mutualist-gut interactions.

Mechanics and Morphology of Proliferating Cell Collectives with Self-Inhibiting Growth

We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring patterns in cell size whose spatiotemporal structure is closely tied to the individual cell's stress response. Motivated by these observations, we derive a multiscale continuum theory whose parameters map directly to the discrete model. Analytical solutions of this theory show the concentric patterns arise from anisotropically accumulated resistance to growth over many cell cycles. This Letter shows how purely mechanical processes can affect the internal patterning and morphology of cell collectives, and provides a concise theoretical framework for connecting the micro- to macroscopic dynamics of proliferating matter.

Micron-scale topographies affect phagocytosis of bacterial cells on polydimethylsiloxane surfaces

Many medical devices implanted in patients to mitigate diseases and medical conditions have different types of topographic features. While appropriate textures can promote the integration of host cells and reduce scar tissue formation, some textured implants with inappropriate topographies have been associated with inflammation, bacterial colonization, or even malignant complications. To better understand how surface topography affects host immune response to colonizing bacteria, a protocol was developed to investigate phagocytosis of bacterial cells attached on polydimethylsiloxane (PDMS) surfaces with different square-shaped recessive patterns. The interaction between activated RAW 264.7 macrophages and Escherichia coli in recessive wells was visualized in 3D using multiple fluorescent markers. The results revealed that there is a threshold dimension of topography, below which phagocytosis of attached bacterial cells is significantly impeded. Specifically, under our experimental condition, up to 100-fold reduction in phagocytosis was observed in square-shaped patterns with 5 µm side length and 10 µm depth compared to the flat control and patterns with 10 µm or longer side length. The spacing between wells also showed significant effects; e.g., phagocytosis in the wells further decreased when spacing increased to 50 µm. These results are helpful for understanding how undesired topographies may contribute to bacterial colonization and thus infection and other associated complications. STATEMENT OF SIGNIFICANCE: Surface topography plays an important role in bacteria-material infections and thus the safety of implantable medical devices. Undesired topographic features can cause biofilm formation and related complications. However, how surface topography affects the capability of host immune cells to clear colonizing bacteria is not well understood. In this study, the interaction between macrophage RAW264.7 and colonizing E. coli cells on polydimethylsiloxane (PDMS) with recessive features is investigated. It was discovered that the size of recessive features and the spacing between these features have significant effects on phagocytosis of bacteria by macrophages. These new results are helpful for understanding the complex interaction among host cells, bacteria, and implanted biomaterials, which will help guide the rational design of safer medical devices.

A Hamilton principle-based model for diffusion-driven biofilm growth

Dense communities of bacteria, also known as biofilms, are ubiquitous in all of our everyday life. They are not only always surrounding us, but are also active inside our bodies, for example in the oral cavity. While some biofilms are beneficial or even necessary for human life, others can be harmful. Therefore, it is highly important to gain an in-depth understanding of biofilms which can be achieved by in vitro or in vivo experiments. Since these experiments are often time-consuming or expensive, in silico models have proven themselves to be a viable tool in assisting the description and analysis of these complicated processes. Current biofilm growth simulations are using mainly two approaches for describing the underlying models. The volumetric approach splits the deformation tensor into a growth and an elastic part. In this approach, the mass never changes, unless some additional constraints are enforced. The density-based approach, on the other hand, uses an evolution equation to update the growing tissue by adding mass. Here, the density stays constant, and no pressure is exerted. The in silico model presented in this work combines the two approaches. Thus, it is possible to capture stresses inside of the biofilm while adding mass. Since this approach is directly derived from Hamilton's principle, it fulfills the first and second law of thermodynamics automatically, which other models need to be checked for separately. In this work, we show the derivation of the model as well as some selected numerical experiments. The numerical experiments show a good phenomenological agreement with what is to be expected from a growing biofilm. The numerical behavior is stable, and we are thus capable of solving complicated boundary value problems. In addition, the model is very reactive to different input parameters, thereby different behavior of various biofilms can be captured without modifying the model.

Two marine sulfur-reducing bacteria co-culture is essential for productive infection by a T4-like Escherichia coli-infecting phage

The control of microbiologically influenced corrosion (MIC) challenges the oil exploration sector. The MIC results from electrochemical reactions facilitated by microorganisms such as sulfate-reducing bacteria (SRB), which adhere to the surface of the ducts forming biofilms. SRB uses sulfate as the final electron acceptor, resulting in hydrogen sulfide as the final product, a highly reactive corrosive, and toxic compound. Due to the high diversity of the SRB group, this study evaluated the effect of an Escherichia coli phage, with biofilm degrading enzymes, in preventing biofilm formation by microbial consortium P48SEP and reducing H2S production in a complex SRB community. Three phage concentrations were evaluated (104, 108 and 1012 UFP/ml). High and medium phage concentrations prevented biofilm development, as evidenced by scanning electron microscopy, chemical analysis, and cell counts. In addition, the virus altered the expression pattern of some bacterial genes and the relative abundance of proteins related to biofilm formation and cell stress response. Using a complex culture formed mainly by SRB, it was possible to observe the bacterial growth, H2S, and metabolic activity reduction after the phage was added. This study shows for the first time the ability of an E. coli-infecting phage to prevent the biofilm formation of an SRB consortium and infect and replicate at high concentrations on the non-specific host. This new finding turns the use of non-specific phages a promising alternative for the control of biocorrosion in oil and gas installations, on the other side, alert to the use of large concentration of phages and the influence on bacterial groups with geological importance, opening a research field in phage biology.

Microbial extracellular polymeric substances in the environment, technology and medicine

Microbial biofilms exhibit a self-produced matrix of extracellular polymeric substances (EPS), including polysaccharides, proteins, extracellular DNA and lipids. EPS promote interactions of the biofilm with other cells and sorption of organics, metals and chemical pollutants, and they facilitate cell adhesion at interfaces and ensure matrix cohesion. EPS have roles in various natural environments, such as soils, sediments and marine habitats. In addition, EPS are relevant in technical environments, such as wastewater and drinking water treatment facilities, and water distribution systems, and they contribute to biofouling and microbially influenced corrosion. In medicine, EPS protect pathogens within the biofilm against the host immune system and antimicrobials, and emerging evidence suggests that EPS can represent potential virulence factors. By contrast, EPS yield a wide range of valuable products that include their role in self-repairing concrete. In this Review, we aim to explore EPS as a functional unit of biofilms in the environment, in technology and in medicine.

Screening and heterologous expression of an antimicrobial peptide SCAK33 with broad-spectrum antimicrobial activity resourced from sea cucumber proteome

Antimicrobial peptides (AMPs) are a family of short defense proteins that are naturally produced by all organisms and have great potential as effective substitutes for small-molecule antibiotics. The present study aims to excavate AMPs from sea cucumbers and achieve their heterologous expression in prokaryotic Escherichia coli. Using MytC as a probe, a cysteine-stabilized peptide SCAK33 with broad-spectrum antimicrobial activity was discovered from the proteome of Apostichopus japonicas. The SCAK33 showed inhibitory effects on both gram positive and gram negative bacteria with MICs of 3-28 μM, and without significant hemolysis activity in rat blood erythrocyte. Especially, it exhibited good antimicrobial activity against Bacillus megaterium, B. subtilis, and Vibrio parahaemolyticus with the MIC of 3, 7, and 7 μM, respectively. After observation by scanning electronic microscopy (SEM) and confocal laser scanning microscope (CLSM), it was found that the cell membrane of bacteria was severely damaged. Furthermore, the recombinant SCAK33 (reSCAK33) was heterologously expressed by fusion with SUMO tag in E. coli BL21(DE3), and the protein yield reached 70 mg/L. The research will supplement the existing quantity of sea cucumber AMPs and provide data support for rapid mining and biological preparation of sea cucumber AMPs.

Mechanism of the antimicrobial activity induced by phosphatase inhibitor sodium ortho-vanadate

The present study describes a novel antimicrobial mechanism based on Sodium Orthovanadate (SOV), an alkaline phosphatase inhibitor. Scanning electron microscopy (SEM), transmission electron microscopy (TEM) and atomic force microscopy (AFM) were employed to examine the surface morphologies of the test organism, Escherichia coli (E. coli), during various antibacterial phases. Our results indicated that SOV kills bacteria by attacking cell wall growth and development, leaving E. coli's outer membrane intact. Our antimicrobial test indicated that the MIC of SOV for both E. coli and Lactococcus lactis (L. lactis) is 40 μM. A combination of quantum mechanical calculations and vibrational spectroscopy revealed that divanadate from SOV strongly coordinates with Ca2+ and Mg2+, which are the activity centers for the phosphatase that regulates bacterial cell wall synthesis. The current study is the first to propose the antibacterial mechanism caused by SOV attacking cell wall.

The evolution of calcified anaerobic granular sludge bed informs the deep insight into its agglomeration process

Calcium-induced agglomeration of anaerobic granular sludge bed (AGSB) has become a critical factor in performance decline of calcified anaerobic reactors. However, the agglomeration process of AGSB and the underlying mechanisms remain unclear and elusive. This study delved into the evolution of calcified AGSB, and four typical states of normal AGSB (Nor-AGSB), calcified dispersed AGSB (Dis-AGSB), calcified dimeric AGSB (Dim-AGSB), and calcified polymeric AGSB (Pol-AGSB) were characterized. It was found that the minimum transport velocity of Dis-AGSB was 3.14-3.79 times higher than that of Nor-AGSB, and surpassed both the superficial velocity and the bubble-induced wake velocity. This led to the sedimentation of AGS at the bottom of reactor, resulting in stable contacts with each other. Solid fillers between AGS, namely cement, were observed within Dim-AGSB and Pol-AGSB, and could be classified as tightly- and loosely- bonded cement (T- and L-cement). Further analysis revealed that T-cement was rich in extracellular polymeric substances and intertwining pili/flagella, serving as the primary driving force for robust inter-AGS adhesion. While the L-cement was primarily in the form of calcite precipitation, and blocked the convective mass transfer pathways in Pol-AGSB, leading to the decreased convective mass transfer capacity. The critical distance between calcite and AGS was further revealed as 5.33 nm to form stable initial adhesion. Consequently, the agglomeration mechanism involving the evolution of AGSB was proposed as calcium-induced sedimentation, calcium-induced adhesion, and calcium-induced stasis in order. This study is expected to offer deep insight into the calcium-induced agglomeration especially from the overlooked perspective of AGSB, and provides feasible control strategies to manage the pressing calcification issues in engineering applications.

Unraveling the role of toxin-antitoxin systems in Burkholderia pseudomallei: exploring bacterial pathogenesis and interactions within the HigBA families

Burkholderia pseudomallei (Bpm) is a Gram-negative intracellular pathogen that causes melioidosis in humans, a neglected, underreported, and lethal disease that can reach a fatal outcome in over 50% of the cases. It can produce both acute and chronic infections, the latter being particularly challenging to eliminate because of the intracellular life cycle of the bacteria and its ability to generate a "persister" dormant state. The molecular mechanism that allows the switch between growing and persister phenotypes is not well understood but it is hypothesized to be due at least in part to the participation of toxin-antitoxin (TA) systems. We have previously studied the link between one of those systems (defined as HigBA) with specific expression patterns associated with levofloxacin antibiotic exposure. Through in silico methods, we predicted the presence of another three pairs of genes encoding for additional putative HigBA systems. Therefore, our main goal was to establish which mechanisms are conserved as well as which pathways are specific among different Bpm TA systems from the same family. We hypothesize that the high prevalence, and sometimes even redundancy of these systems in the Bpm chromosomes indicates that they can interact with each other and not function as only individual systems, as it was traditionally thought, and might be playing an undefined role in Bpm lifecycle. Here, we show that both the toxin and the antitoxin of the different systems contribute to bacterial survival and that toxins from the same family can have a cumulative effect under environmental stressful conditions.

IMPORTANCE

Toxin-antitoxin (TA) systems play a significant role in bacterial persistence, a phenomenon where bacterial cells enter a dormant or slow-growing state to survive adverse conditions such as nutrient deprivation, antibiotic exposure, or host immune responses. By studying TA systems in Burkholderia pseudomallei, we can gain insights into how this pathogen survives and persists in the host environment, contributing to its virulence and ability to cause melioidosis chronic infections.

The combination of allicin with domiphen is effective against microbial biofilm formation

Background

Microorganisms in biofilms are particularly difficult to control because of their increased survival and antibiotic resistance. Allicin and domiphen were employed to inhibit the microbial growth and biofilm formation of Staphylococcus aureus, Escherichia coli, and Candida albicans strains.

Methods

Broth microdilution method and checkerboard assay were conducted to determine the efficacy of allicin combined with domiphen against S. aureus, E. coli, and C. albicans. Microbial biofilm formation was measured using the crystal violet staining method and fluorescence microscopy. And the total viable count of the biofilm cells on material surface after the treatment with antimicrobial reagents was calculated with the plate count technique.

Results

The two drugs showed synergistic effects against the pathogens with a fractional bactericidal concentration of less than 0.38. The combination of 64 μg/mL allicin with 1 μg/mL domiphen dispersed over 50% of the biofilm mass of S. aureus, E. coli, and C. albicans. In addition, the drug combination reduced the total viable counts of E. coli and C. albicans biofilm cells on stainless steel and polyethylene surfaces by more than 102 CFU/mL.

Conclusion

The combination of allicin and domiphen is an effective strategy for efficiently decreasing biofilms formation on various industrial materials surfaces.

Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms

Living active collectives have evolved with remarkable self-patterning capabilities to adapt to the physical and biological constraints crucial for their growth and survival. However, the intricate process by which complex multicellular patterns emerge from a single founder cell remains elusive. In this study, we utilize an agent-based model, validated through single-cell microscopy imaging, to track the three-dimensional (3D) morphodynamics of cells within growing bacterial biofilms encased by agarose gels. The confined growth conditions give rise to a spatiotemporally heterogeneous stress landscape within the biofilm. In the core of the biofilm, where high hydrostatic and low shear stresses prevail, cell packing appears disordered. In contrast, near the gel-cell interface, a state of high shear stress and low hydrostatic stress emerges, driving nematic ordering, albeit with a time delay inherent to shear stress relaxation. Strikingly, we observe a robust spatiotemporal correlation between stress anisotropy and nematic ordering within these confined biofilms. This correlation suggests a mechanism whereby stress anisotropy plays a pivotal role in governing the spatial organization of cells. The reciprocity between stress anisotropy and cell ordering in confined biofilms opens new avenues for innovative 3D mechanically guided patterning techniques for living active collectives, which hold significant promise for a wide array of environmental and biomedical applications.

Interplay between environmental yielding and dynamic forcing modulates bacterial growth

Many bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly tunable structural and rheological properties, under different amounts of external forcing imposed by mechanical shaking, and in both aerobic and anaerobic conditions. Our experiments establish a general principle: that the balance between the yield stress of the environment that the cells inhabit, σy, and the external stress imposed on the environment, σ, modulates bacterial growth by altering transport of essential nutrients to the cells. In particular, when σy<σ, the environment is easily fluidized and mixed over large scales, providing nutrients to the cells and sustaining complete cellular growth. By contrast, when σy>σ, the elasticity of the environment suppresses large-scale fluid mixing, limiting nutrient availability and arresting cellular growth. Our work thus reveals a new mechanism, beyond effects that change cellular behavior via local forcing, by which the rheology of the environment may modulate microbial physiology in diverse natural and industrial settings.

Microbes in porous environments: from active interactions to emergent feedback

Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.

Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose

To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.

Obstructed swelling and fracture of hydrogels

Obstructions influence the growth and expansion of bodies in a wide range of settings-but isolating and understanding their impact can be difficult in complex environments. Here, we study obstructed growth/expansion in a model system accessible to experiments, simulations, and theory: hydrogels swelling around fixed cylindrical obstacles with varying geometries. When the obstacles are large and widely-spaced, hydrogels swell around them and remain intact. In contrast, our experiments reveal that when the obstacles are narrow and closely-spaced, hydrogels fracture as they swell. We use finite element simulations to map the magnitude and spatial distribution of stresses that build up during swelling at equilibrium in a 2D model, providing a route toward predicting when this phenomenon of self-fracturing is likely to arise. Applying lessons from indentation theory, poroelasticity, and nonlinear continuum mechanics, we also develop a theoretical framework for understanding how the maximum principal tensile and compressive stresses that develop during swelling are controlled by obstacle geometry and material parameters. These results thus help to shed light on the mechanical principles underlying growth/expansion in environments with obstructions.

Proteomic profile of Cryptococcus gattii biofilm: Metabolic shift and the potential activation of electron chain transport

Cryptococcus gattii is a primary pathogenic fungus that causes pneumonia. This species is also responsible for an outbreak in Vancouver, Canada, and spreading to the mainland and United States. The use of medical devices is often complicated by infections with biofilm-forming microbes with increased resistance to antimicrobial agents and host defense mechanisms. This study investigated the comparative proteome of C. gattii R265 (VGIIa) grown under planktonic and biofilm conditions. A brief comparison with C. neoformans H99 biofilm and the use of different culture medium and surface were also evaluated. Using Multidimensional Protein Identification Technology (MudPIT), 1819 proteins were identified for both conditions, where 150 (8.2%) were considered differentially regulated (up- or down-regulated and unique in biofilm cells). Overall, the proteomic approach suggests that C. gattii R265 biofilm cells are maintained by the induction of electron transport chain for reoxidation, and by alternative energy metabolites, such as succinate and acetate. SIGNIFICANCE: Since C. gattii is considered a primary pathogen and is one of the most virulent and less susceptible to antifungals, understanding how biofilms are maintained is fundamental to search for new targets to control this important mode of growth that is difficult to eradicate.

Are Escherichia coli causing recurrent cystitis just ordinary Uropathogenic E. coli (UPEC) strains?

Specific determinants associated with Uropathogenic Escherichia coli (UPEC) causing recurrent cystitis are still poorly characterized. The aims of this study were (i) to describe genomic and phenotypic traits associated with recurrence using a large collection of recurrent and paired sporadic UPEC isolates, and (ii) to explore within-host genomic adaptation associated with recurrence using series of 2 to 5 sequential UPEC isolates. Whole genome comparative analyses between 24 recurrent cystitis isolates (RCIs) and 24 phylogenetically paired sporadic cystitis isolates (SCIs) suggested a lower prevalence of putative mobile genetic elements (MGE) in RCIs, such as plasmids and prophages. The intra-patient evolution of the 24 RCI series over time was characterized by SNP occurrence in genes involved in metabolism or membrane transport, and by plasmid loss in 5 out of the 24 RCI series. Genomic evolution occurred early in the course of recurrence, suggesting rapid adaptation to strong selection pressure in the urinary tract. However, RCIs did not exhibit specific virulence factor determinants and could not be distinguished from SCIs by their fitness, biofilm formation, or ability to invade HTB-9 bladder epithelial cells. Taken together, these results suggest a rapid but not convergent adaptation of RCIs that involves both strain- and host-specific characteristics.

Interfacial morphodynamics of proliferating microbial communities

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.

Revisiting ESKAPE Pathogens: virulence, resistance, and combating strategies focusing on quorum sensing

The human-bacterial association is long-known and well-established in terms of both augmentations of human health and attenuation. However, the growing incidents of nosocomial infections caused by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) call for a much deeper understanding of these organisms. Adopting a holistic approach that includes the science of infection and the recent advancements in preventing and treating infections is imperative in designing novel intervention strategies against ESKAPE pathogens. In this regard, this review captures the ingenious strategies commissioned by these master players, which are teamed up against the defenses of the human team, that are equally, if not more, versatile and potent through an analogy. We have taken a basketball match as our analogy, dividing the human and bacterial species into two teams playing with the ball of health. Through this analogy, we make the concept of infectious biology more accessible.

Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology

The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.

Ferritinophagy-mediated iron competition in RUTIs: Tug-of-war between UPEC and host

Uropathogenic Escherichia coli (UPEC) is the main pathogen of recurrent urinary tract infections (RUTIs). Urinary tract infection is a complicated interaction between UPEC and the host. During infection, UPEC can evade the host's immune response and retain in bladder epithelial cells, which requires adequate nutritional support. Iron is the first necessary trace element in life and a key nutritional factor, making it an important part of the competition between UPEC and the host. On the one hand, UPEC grabs iron to satisfy its reproduction, on the other hand, the host relies on iron to build nutritional immunity defenses against UPEC. Ferritinophagy is a selective autophagy of ferritin mediated by nuclear receptor coactivator 4, which is not only a way for the host to regulate iron metabolism to maintain iron homeostasis, but also a key point of competition between the host and UPEC. Although recent studies have confirmed the role of ferritinophagy in the progression of many diseases, the mechanism of potential interactions between ferritinophagy in UPEC and the host is poorly understood. In this paper, we reviewed the potential mechanisms of ferritinophagy-mediated iron competition in the UPEC-host interactions. This competitive relationship, like a tug-of-war, is a confrontation between the capability of UPEC to capture iron and the host's nutritional immunity defense, which could be the trigger for RUTIs. Therefore, understanding ferritinophagy-mediated iron competition may provide new strategies for exploring effective antibiotic alternative therapies to prevent and treat RUTIs.

Habitat complexity affects microbial growth in fractal maze

The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.

Extracellular Matrix Rigidities Regulate the Tricarboxylic Acid Cycle and Antibiotic Resistance of Three-Dimensionally Confined Bacterial Microcolonies

As a major cause of clinical chronic infection, microbial biofilms/microcolonies in host tissues essentially live in 3D-constrained microenvironments, which potentially modulate their spatial self-organization and morphodynamics. However, it still remains unclear whether and how mechanical cues of 3D confined microenvironments, for example, extracellular matrix (ECM) stiffness, exert an impact on antibiotic resistance of bacterial biofilms/microcolonies. With a high-throughput antibiotic sensitivity testing (AST) platform, it is revealed that 3D ECM rigidities greatly modulate their resistance to diverse antibiotics. The microcolonies in 3D ECM with human tissue-specific rigidities varying from 0.5 to 20 kPa show a ≈2-10 000-fold increase in minimum inhibitory concentration, depending on the types of antibiotics. The authors subsequently identified that the increase in 3D ECM rigidities leads to the downregulation of the tricarboxylic acid (TCA) cycle, which is responsible for enhanced antibiotic resistance. Further, it is shown that fumarate, as a potentiator of TCA cycle activity, can alleviate the elevated antibiotic resistance and thus remarkably improve the efficacy of antibiotics against bacterial microcolonies in 3D confined ECM, as confirmed in the chronic infection mice model. These findings suggest fumarate can be employed as an antibiotic adjuvant to effectively treat infections induced by bacterial biofilms/microcolonies in a 3D-confined environment.

Hierarchical encapsulation of bacteria in functional hydrogel beads for inter- and intra- species communication

To sequester prokaryotic cells in a biofilm-like niche, the creation of a pertinent and reliable microenvironment that reflects the heterogeneous nature of biological systems is vital for sustenance. Design of a microenvironment that is conducive for growth and survival of organisms, should account for factors such as mass transport, porosity, stability, elasticity, size, functionality, and biochemical characteristics of the organisms in the confined architecture. In this work we present an artificial long-term confinement model fabricated by natural alginate hydrogels that are structurally stable and can host organisms for over 10 days in physiologically relevant conditions. A unique feature of the confinement platform is the development of stratified habitats wherein bacterial cells can be entrapped in the core as well as in the shell layers, wherein the thickness and the number of shell layers are tunable at fabrication. We show that the hydrogel microenvironment in the beads can host complex subpopulations of organisms similar to that in a biofilm. Dynamic interaction of bacterial colonies encapsulated in different beads or within the core and stratified layers of single beads was demonstrated to show intra- species communication. Inter- species communication between probiotic bacteria and human colorectal carcinoma cells was also demonstrated to highlight a possible bidirectional communication between the organisms in the beads and the environment. STATEMENT OF SIGNIFICANCE: Bacteria confinement in a natural soft hydrogel structure has always been a challenge due to the collapse of hydrogel architectures. Alternative methods have been attempted to encapsulate microorganisms by employing various processes to avoid/minimize rupturing of hydrogel structures. However, most of the past approaches have been unfavorable in balancing cell proliferation and functionality upon confinement. Our study addresses the fundamental gap in knowledge necessary to create favorable and complex 3D biofilm mimics utilizing natural hydrogel for microbial colonization for long-term studies. Our approach represents a cornerstone in the development of 3D functional architectures not only to advance studies in microbial communication, host-microbe interaction but also to address basic and fundamental questions in biology.

Improving mechanical stability of anammox granules with organic stress by limited filamentous bulking

Under organic stress, the limited filamentous bulking (FB) was demonstrated to improve anammox capability by inhibiting granule disintegration and washout. The accumulation of internal stress played a more important role than the adverse physicochemical properties (low viscoelasticity and hydrophobicity) of granules in limiting granular strength by consuming the granular elastic energy. Different from the floc-forming heterotrophic bacteria (HB) that stored its growth stress as internal stress by pushing the surrounded anammox micro-colonies outwards under the spatial constraint of elastic anammox "shell", the filamentous HB grew into a uniform network structure within granules, endowed granules low internal stress and acted as the granular skeleton due to its rich amyloid substance, which was benefited from the elimination of inhomogeneous growth and the consequent expansion competition for living space. Combined with the mechanical instability and sticking-spring models, controlling FB at limited level was effective for improving granular strength without affecting sludge-water separation.

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.

Self-locomotive, antimicrobial microrobot (SLAM) swarm for enhanced biofilm elimination

Biofilm is a major cause of infections and infrastructure deterioration, largely due to molecular diffusion restrictions that hamper the antimicrobial activity of traditional antibiotics and disinfectants. Here, we present a self-locomotive, antimicrobial microrobot (SLAM) swarm that can penetrate, fracture, and detach biofilm and, in turn, nullify bacterial resistance to antibiotics. The SLAM is assembled by loading a controlled mass of manganese oxide nanosheets on diatoms with the polydopamine binder. In hydrogen peroxide solution, SLAMs produce oxygen bubbles that generate thrust to penetrate the rigid and dense Pseudomonas aeruginosa biofilm and self-assemble into a swarm that repeatedly surrounds, expands, and bursts oxygen bubbles. The resulting cavities continue to deform and fracture extracellular polymeric substances from microgrooved silicone substrates and wounded skin explants while decreasing the number of viable bacterial cells. Additionally, SLAM allows irrigating water or antibiotics to access the residual biofilm better, thus enhancing the synergistic efficacy in killing up to 99.9% of bacterial cells.

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.

A Microfluidic Chip for Studies of the Dynamics of Antibiotic Resistance Selection in Bacterial Biofilms

Biofilms are arguably the most important mode of growth of bacteria, but how antibiotic resistance emerges and is selected in biofilms remains poorly understood. Several models to study evolution of antibiotic resistance have been developed, however, their usability varies depending on the nature of the biological question. Here, we developed and validated a microfluidic chip (Brimor) for studying the dynamics of enrichment of antibiotic-resistant bacteria in biofilms using real-time monitoring with confocal microscopy. In situ extracellular cellulose staining and physical disruption of the biomass confirmed Escherichia coli growth as biofilms in the chip. We showed that seven generations of growth occur in 16 h when biofilms were established in the growth chambers of Brimor, and that bacterial death and growth rates could be estimated under these conditions using a plasmid with a conditional replication origin. Additionally, competition experiments between antibiotic-susceptible and -resistant bacteria at sub-inhibitory concentrations demonstrated that the antibiotic ciprofloxacin selected for antibiotic resistance in bacterial biofilms at concentrations 17-fold below the minimal inhibitory concentration of susceptible planktonic bacteria. Overall, the microfluidic chip is easy to use and a relevant model for studying the dynamics of selection of antibiotic resistance in bacterial biofilms and we anticipate that the Brimor chip will facilitate basic research in this area.

Nutrient starvation intensifies chlorine disinfection-stressed biofilm formation

Bacterial surface attachment and subsequent biofilm expansion represent an essential adaptation to environmental signals and stresses, which are of great concern for many natural and engineered ecosystems. Yet the underlying mechanisms and driving forces of biofilm formation in a chlorinated and nutrient-restricted system remain sketchy. In this study, we coupled an experimental investigation and modeling simulation to understand how chlorination and nutrient limitation conspire to form biofilm using Pseudomonas aeruginosa as a model bacterium. Experimental results showed that moderate chlorination at 1.0 mg/L led to biofilm development amplified to 2.6 times of those without chlorine, while additional nutrient limitation (of 1/50-diluted or 0.4 g/L LB broth culture) achieved 4.6 times increment as compared to those of undiluted scenarios (of 20 g/L LB broth culture) with absence of chlorination after 24 h exposure. Meanwhile, intermediate chlorination stimulated instant flagellar motility and subsequently extracellular polymeric substances (EPS) secretion, particularly under limited nutrient condition (of 1/50-diluted or 0.4 g/L LB broth culture) that retarded chlorine consumption and provoked bacterial nutrient-limitation response. From our simulations, chlorine and resource levels along with associated spatio-temporal variations collectively drove bacterial cell movement and EPS excretion. Our results demonstrated that restraining nutrient intensified chlorination-excited cell movement and EPS production that reinforced biological and cell-surface interactions, thereby encouraging bacterial surface attachment and subsequent biofilm development. The findings provide the insights into the linkage of disinfectant and nutrient-regulated bacterial functional responses with consequent micro-habitats and biofilm dynamics.

High burden and diversity of carbapenemase-producing Enterobacterales observed in wastewater of a tertiary care hospital in Germany

Hospitals are one of the main reservoirs of multi-resistant Enterobacterales (MRE). As MRE are resistant to the most frequently used antibiotics, therapy for patients with MRE infections is challenging. It has been previously described that MRE from hospital wastewater can pass into municipal wastewater and even surface water. In this study, we investigated the diversity and epidemiology of MRE in the wastewater of a large tertiary care hospital. Wastewater samples were collected for a four-day period and tested for the presence of Enterobacterales resistant to 3rd gen. cephalosporins. Representative isolates were further characterized by whole genome sequencing. In 120 β-glucuronidase-producing isolates, 68 Escherichia coli and, interestingly, also 52 Citrobacter freundii were identified. In 120 β-glucosidase-producing isolates 45 Serratia marcescens, 34 Klebsiella oxytoca, 32 Enterobacter cloacae and 9 Klebsiella pneumoniae were observed. For all species various MLST sequence types and different clusters of resistance genes were determined, showing a great diversity within the different Enterobacterales, further corroborated by clonal analysis performed by cgMLST. The most prominent clone was wastewater associated E. coli ST635, which accounted for 47.1% of all E. coli isolates. Interestingly, 45.6% of E. coli, 88.5% of C. freundii, 95.6% of S. marcescens, 91.2% of K. oxytoca, 96.9% of E. cloacae and 88.9% of K. pneumoniae isolates carried a carbapenemase gene, indicating a high burden with carbapenemase-producing Enterobacterales. Comparison with clinical isolates from the same hospital displayed few clonal matches. One wastewater isolate of K. pneumoniae was identified to be closely related compared to a clone that had been introduced into the hospital during an outbreak four years earlier. One E. coli isolate was identified as identical to an isolate from a patient, with inpatient stay during the sampling period. The data obtained in this study highlight the problem of antibiotic resistance of Enterobacterales in hospital wastewater. In particular, the clustered occurrence of carbapenemase genes is of great concern and underscores the problem of increasingly scarce antibiotic options against these bacteria.

Macromolecular crowding limits growth under pressure

Cells that grow in confined spaces eventually build up mechanical compressive stress. This growth-induced pressure (GIP) decreases cell growth. GIP is important in a multitude of contexts from cancer, to microbial infections, to biofouling, yet our understanding of its origin and molecular consequences remains limited. Here, we combine microfluidic confinement of the yeast Saccharomyces cerevisiae, with rheological measurements using genetically encoded multimeric nanoparticles (GEMs) to reveal that growth-induced pressure is accompanied with an increase in a key cellular physical property: macromolecular crowding. We develop a fully calibrated model that predicts how increased macromolecular crowding hinders protein expression and thus diminishes cell growth. This model is sufficient to explain the coupling of growth rate to pressure without the need for specific molecular sensors or signaling cascades. As molecular crowding is similar across all domains of life, this could be a deeply conserved mechanism of biomechanical feedback that allows environmental sensing originating from the fundamental physical properties of cells.

Comparative Study of Polycaprolactone Electrospun Fibers and Casting Films Enriched with Carbon and Nitrogen Sources and Their Potential Use in Water Bioremediation

Augmenting bacterial growth is of great interest to the biotechnological industry. Hence, the effect of poly (caprolactone) fibrous scaffolds to promote the growth of different bacterial strains of biological and industrial interest was evaluated. Furthermore, different types of carbon (glucose, fructose, lactose and galactose) and nitrogen sources (yeast extract, glycine, peptone and urea) were added to the scaffold to determinate their influence in bacterial growth. Bacterial growth was observed by scanning electron microscopy; thermal characteristics were also evaluated; bacterial cell growth was measured by ultraviolet-visible spectrophotometry at 600-nm. Fibers produced have an average diameter between 313 to 766 nm, with 44% superficial porosity of the scaffolds, a glass transition around ~64 °C and a critical temperature of ~338 °C. The fibrous scaffold increased the cell growth of Escherichia coli by 23% at 72 h, while Pseudomonas aeruginosa and Staphylococcus aureus increased by 36% and 95% respectively at 48 h, when compared to the normal growth of their respective bacterial cultures. However, no significant difference in bacterial growth between the scaffolds and the casted films could be observed. Cell growth depended on a combination of several factors: type of bacteria, carbon or nitrogen sources, casted films or 3D scaffolds. Microscopy showed traces of a biofilm formation around 3 h in culture of P. aeruginosa. Water bioremediation studies showed that P. aeruginosa on poly (caprolactone)/Glucose fibers was effective in removing 87% of chromium in 8 h.

Scale-dependent tipping points of bacterial colonization resistance

The commonly observed stability of natural microbiomes is important for their function, yet the ubiquity of microbiome stability remains enigmatic. The strongest form of stability, colonization resistance, protects residents against invaders and is often associated with specific porous structures, such as skin follicles or intestinal crypts. By systematically probing the colonization of fly gut–derived bacteria in microfluidic pores of varying sizes, we revealed that colonization patterns and invasion rates strongly depend on the pore size. Mathematical modeling shows that bacteria spontaneously tend to organize into a dense colonization-resistant state in pores exceeding a critical size. The scale dependence of stability and resilience could bias ecological filtering in microbiomes and should be considered in the design of microbial ecology experiments.

Bacteria are efficient colonizers of a wide range of secluded microhabitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity of these habitats modulates microbial self-organization remains poorly understood, in part because of the difficulty to precisely manipulate the physical structure of microbial environments. Using a microfluidic device to grow bacteria in crypt-like incubation chambers of systematically varied lengths, we show that small variations in the physical structure of the microhabitat can drastically alter bacterial colonization success and resistance against invaders. Small crypts are uncolonizable; intermediately sized crypts can stably support dilute populations, while beyond a second critical length scale, populations phase separate into a dilute region and a jammed region. The jammed state is characterized by extreme colonization resistance, even if the resident strain is suppressed by an antibiotic. Combined with a flexible biophysical model, we demonstrate that colonization resistance and associated priority effects can be explained by a crowding-induced phase transition, which results from a competition between proliferation and density-dependent cell leakage. The emerging sensitivity to scale underscores the need to control for scale in microbial ecology experiments. Systematic flow-adjustable length-scale variations may serve as a promising strategy to elucidate further scale-sensitive tipping points and to rationally modulate the stability and resilience of microbial colonizers.

Active Extensile Stress Promotes 3D Director Orientations and Flows

We use numerical simulations and linear stability analysis to study an active nematic layer where the director is allowed to point out of the plane. Our results highlight the difference between extensile and contractile systems. Contractile stress suppresses the flows perpendicular to the layer and favors in-plane orientations of the director. By contrast extensile stress promotes instabilities that can turn the director out of the plane, leaving behind a population of distinct, in-plane regions that continually elongate and divide. This supports extensile forces as a mechanism for the initial stages of layer formation in living systems, and we show that a planar drop with extensile (contractile) activity grows into three dimensions (remains in two dimensions). The results also explain the propensity of disclination lines in three dimensional active nematics to be of twist type in extensile or wedge type in contractile materials.

Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters

Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.

Extracellular matrix stiffness modulates host-bacteria interactions and antibiotic therapy of bacterial internalization

Pathogenic bacteria evolve multiple strategies to hijack host cells for intracellular survival and persistent infections. Previous studies have revealed the intricate interactions between bacteria and host cells at genetic, biochemical and even single molecular levels. Mechanical interactions and mechanotransduction exert a crucial impact on the behaviors and functions of pathogenic bacteria and host cells, owing to the ubiquitous mechanical microenvironments like extracellular matrix (ECM) stiffness. Nevertheless, it remains unclear whether and how ECM stiffness modulates bacterial infections and the sequential outcome of antibacterial therapy. Here we show that bacteria tend to adhere to and invade epithelial cells located on the regions with relatively high traction forces. ECM stiffness regulates spatial distributions of bacteria during the invasion through arrangements of F-actin cytoskeletons in host cells. Depolymerization of cytoskeletons in the host cells induced by bacterial infection decreases intracellular accumulation of antibiotics, thus preventing the eradication of invaded bacterial pathogens. These findings not only reveal the key regulatory role of ECM stiffness, but suggest that the coordination of cytoskeletons may provide alternative approaches to improve antibiotic therapy against multidrug resistant bacteria in clinic.

PrbP modulates biofilm formation in Liberibacter crescens

In Liberibacter asiaticus, PrbP is a transcriptional regulatory protein involved in survival and persistence during host infection. Tolfenamic acid was previously found to inhibit interactions between PrbP and the promotor region of rplK, resulting in reduced survival of L. asiaticus in the citrus host. In this study, we performed transcriptome analyses to elucidate the PrbP regulon in L. crescens, as it is phylogenetically the closest related species to L. asiaticus that can be grown in laboratory conditions. Chemical inhibition of PrbP with tolfenamic acid revealed that PrbP is involved in the regulation of diverse cellular processes, including stress response, cell motility, cell cycle and biofilm formation. In vitro DNA binding and bacterial two-hybrid assays also suggested that PrbP is a global regulator of multiple transcription factors (RpoH, VisN, PleD, MucR, MocR and CtrA) at both transcriptional and/or post-transcriptional levels. Sub-lethal concentrations of tolfenamic acid significantly reduced the attachment of L. crescens during biofilm formation and decreased long-term persistence in biofilm structures. Overall, our findings show the importance of PrbP in regulating diverse biological processes through direct and indirect interactions with other transcriptional regulators in L. crescens.

Effects of Wi-Fi Radiofrequency Radiation on Carbapenem-Resistant Klebsiella pneumoniae

The hazardous consequences of electromagnetic field (EMF) exposure represent a public health concern. Common sources of EMF include smartphones and wireless fidelity (Wi-Fi). The aim of our study is to assess whether exposure to Wi-Fi radiofrequency radiation influences the pathogenic traits of carbapenem-resistant Klebsiella pneumoniae. The susceptibility to antibiotics was evaluated by the determination of minimum inhibitory concentrations (MIC). In this study, K. pneumoniae showed a non-linear response to treatments with Colistin and Gentamycin following different Wi-Fi exposure periods. Transmission electron microscopy revealed morphological changes in the bacterial cell membrane within 24 h of Wi-Fi exposure. Crystal violet quantification and quantitative real-time polymerase chain reaction showed that the ability to form biofilms was greater in Wi-Fi exposed K. pnemoniae when compared to control. Moreover, higher levels of bcsA, mrkA, and luxS messenger RNAs were observed. Our data suggest that Wi-Fi exposure can influence bacteria in a stressful way, leading to an alteration in their antibiotic susceptibility, morphological changes, and cumulative biofilm formation. © 2021 Bioelectromagnetics Society.

Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs

Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.

Biophysical determinants of biofilm formation in the gut

The gastrointestinal (GI) tract harbors the most complex microbial ecosystem in the human body. The mucosal layer that covers the GI tract serves as a polymer-based defensive barrier that prevents the microbiome from reaching the epithelium and disseminating inside the body. Colonization of the mucus may result in the formation of structured polymicrobial communities or biofilms, a hallmark in pathologies such as colorectal cancer, inflammatory bowel disease, and chronic gut wounds. However, the mechanisms by which multispecies biofilms establish on the gut mucosa is unknown. Whether mucus-associated biofilms exist as part of a healthy mucosal barrier is still debated. Here, we discuss the impact that diet and microbial-derived polymers has on mucus structure and microcolony formation and highlight relevant biophysical forces that further shape nascent biofilms.

Monodisperse Selectively Permeable Hydrogel Capsules Made from Single Emulsion Drops

Capsules are often used to protect chemical and biological entities from the environment, to control the timing and location of their release, or to facilitate the collection of waste. Their performance depends on the thickness and composition of their shells, which can be closely controlled if capsules are made from double emulsion drops that are produced with microfluidics. However, the fabrication of such double emulsions is delicate, limiting throughput and increasing costs. Here, a fast, scalable method to produce monodisperse microcapsules possessing mechanically robust, thin, semipermeable hydrogel shells from single emulsion drops is introduced. This is achieved by selectively polymerizing reagents in close proximity to the drop surface to form a biocompatible 1.6 μm-thick hydrogel shell that encompasses a liquid core. The size-selective permeability of the shell enables the growth of living yeast and bacteria in their cores. Moreover, if capsules are loaded with adsorbents, they can repetitively remove waste products from water. The simplicity and robustness of the capsule fabrication makes the process scalable and cost effective. It has thus the potential to extend the use of calibrated capsules possessing well-defined dimensions to cost sensitive fields, including food, waste water treatment, or oil recovery.

Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms

Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.

Effects of Hydrophilicity, Adhesion Work, and Fluid Flow on Biofilm Formation of PDMS in Microfluidic Systems

Polydimethylsiloxane (PDMS) has been the most widely used material in microfluidic systems, especially for cell biology applications. However, the antibacterial performance of PDMS in flow conditions has never been reported in the literature. In this paper, we analyzed the effects of contact angle (CA), adhesion force (work), and surface free energy on the antibacterial activities of PDMS by varying the ratio of curing agents (crosslinking degree) and surface modification with oxygen plasma. The results show that the Young's modulus has no particular effects on bacterial adhesion compared to the CAs of samples. For the first time, we analyzed the adhesion work (AW) effect on biofilm formation, and we found that biofilms tend to form on the surface with less AW. Furthermore, we analyzed the dual effect of hydrophilicity and shear force induced by fluid flow on the bacterial adhesion in PDMS microfluidic systems. We found that at low flow rates in microfluidic conditions, the adhesion of the bacteria on the PDMS surface is inhibited when the fluid flow exceeds a certain value. It required higher shear force to inhibit bacterial adhesion on the hydrophilic surface than on the hydrophobic surface. Therefore, hydrophilicity might be the dominant factor affecting bacterial adhesion.

Bacterial Biofilm Formation Using PCL/Curcumin Electrospun Fibers and Its Potential Use for Biotechnological Applications

Electrospun nanofibers are used for many applications due to their large surface area, mechanical properties, and bioactivity. Bacterial biofilms are the cause of numerous problems in biomedical devices and in the food industry. On the other hand, these bacterial biofilms can produce interesting metabolites. Hence, the objective of this study is to evaluate the efficiency of poly (Ɛ- caprolactone)/Curcumin (PCL/CUR) nanofibers to promote bacterial biofilm formation. These scaffolds were characterized by scanning electron microscopy (SEM), which showed homogeneous fibers with diameters between 441-557 nm; thermogravimetric analysis and differential scanning calorimetry (TGA and DSC) demonstrated high temperature resilience with degradation temperatures over >350 °C; FTIR and ¹H-NMR serve as evidence of CUR incorporation in the PCL fibers. PCL/CUR scaffolds successfully promoted the formation of Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa biofilms. These results will be valuable in the study of controlled harvesting of pathogenic biofilms as well as in metabolites production for biotechnological purposes.

Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains

Deinococcus metallilatus MA1002 was exposed to ultraviolet radiation to generate mutants with enhanced biofilm production. Two strains (nos 5 and 6) were then selected based on their high biofilm formation, as well as their possession of higher concentrations of extracellular matrix components (eDNA, protein and saccharides) than the wild-type (WT). Genomic sequencing revealed the presence of large genome deletions in a secondary chromosome in the mutants. Expression analyses of the WT and mutant strains indicated the upregulation of genes associated with exopolysaccharide synthesis and stress response. The mutant strains showed high mortality in glucose-supplemented (TYG) medium; however, cell death and biofilm formation were not increased in mutant cells grown under acetate- or glyoxylate-added media, suggesting that metabolic toxicity during glucose metabolism induced a high rate of cell death but improved biofilm formation in mutant strains. In damaged cells, eDNAs contributed to the enhanced biofilm formation of D. metallilatus.

The Exo-Polysaccharide Component of Extracellular Matrix is Essential for the Viscoelastic Properties of Bacillus subtilis Biofilms

Bacteria are known to form biofilms on various surfaces. Biofilms are multicellular aggregates, held together by an extracellular matrix, which is composed of biological polymers. Three principal components of the biofilm matrix are exopolysaccharides (EPS), proteins, and nucleic acids. The biofilm matrix is essential for biofilms to remain organized under mechanical stress. Thanks to their polymeric nature, biofilms exhibit both elastic and viscous mechanical characteristics; therefore, an accurate mechanical description needs to take into account their viscoelastic nature. Their viscoelastic properties, including during their growth dynamics, are crucial for biofilm survival in many environments, particularly during infection processes. How changes in the composition of the biofilm matrix affect viscoelasticity has not been thoroughly investigated. In this study, we used interfacial rheology to study the contribution of the EPS component of the matrix to viscoelasticity of Bacillus subtilis biofilms. Two strategies were used to specifically deplete the EPS component of the biofilm matrix, namely (i) treatment with sub-lethal doses of vitamin C and (ii) seamless inactivation of the eps operon responsible for biosynthesis of the EPS. In both cases, the obtained results suggest that the EPS component of the matrix is essential for maintaining the viscoelastic properties of bacterial biofilms during their growth. If the EPS component of the matrix is depleted, the mechanical stability of biofilms is compromised and the biofilms become more susceptible to eradication by mechanical stress.

Do Mixed-Species Biofilms Dominate in Chronic Infections?-Need for in situ Visualization of Bacterial Organization

Chronic infections present a serious economic burden to health-care systems. The severity and prevalence of chronic infections are continuously increasing due to an aging population and an elevated number of lifestyle related diseases such as diabetes. Treatment of chronic infections has proven difficult, mainly due to the presence of biofilms that render bacteria more tolerant toward antimicrobials and the host immune response. Chronic infections have been described to harbor several different bacterial species and it has been hypothesized that microscale interactions and mixed-species consortia are present as described for most natural occurring biofilms i.e., aquatic systems and industrial settings, but also for some commensal human biofilms i.e., the mouth microbiota. However, the presence of mixed-species biofilms in chronic infections is most often an assumption based on culture-based methods and/or by means of molecular approaches, such as PCR and sequencing performed from homogenized bulk tissue samples. These methods disregard the spatial organization of the bacterial community and thus valuable information on biofilm aggregate composition, spatial organization, and possible interactions between different species is lost. Hitherto, only few studies have made visual in situ presentations of mixed-species biofilms in chronic infections, which is pivotal for the description of bacterial composition, spatial distribution, and interspecies interaction on the microscale. In order for bacteria to interact (synergism, commensalism, mutualism, competition, etc.) they need to be in close proximity to each other on the scale where they can affect e.g., solute concentrations. We argue that visual proof of mixed species biofilms in chronic infections is scarce compared to what is seen in e.g., environmental biofilms and call for a debate on the importance of mixed-species biofilm in chronic infections.

Flagellar motility mediates early-stage biofilm formation in oligotrophic aquatic environment

Flagellar motility enables resource acquisition and noxious substance evasion, underpinning imperative ecological processes in aquatic environments. Yet the underlying mechanism that links flagellar motility with surface attachment and thereby biofilm formation, especially in conditions of limited resource availability, remains elusive. Here, we present experimental and modeling evidence to unveil bacterial motility and biofilm formation under nutrient-limited stresses with Pseudomonas aeruginosa (WT) and its nonflagellated isogenic mutant (ΔfliC) as model bacteria. Results revealed that boosted flagellar motility of WT strain promoted biofilm initialization to a peak value of 0.99 × 10⁷ cells/cm² at 1/50 dilution after 20 min incubation. We hypothesized that bacteria can invoke instant motility acceleration for survival confronting nutrient-limited stress, accompanied by optimized chemotactic foraging through sensing ambient chemical gradients. Accordingly, accelerated cell motility in oligotrophic environment created increased cell-cell and cell-surface interactions and thereof facilitated biofilm initialization. It was confirmed by the consistence of modeling predictions and experimental results of cell velocity and surface attachment. With the development of biofilm, promotion effect of flagellar motility responding to nutrient deprivation-stress faded out. Instead, loss of motility profiting increased growth rates and extracellular protein excretion, associated with an enhancement of biofilm development for the mutant in oligotrophic aquatic environment. For both strains, nutrient limitation evidently reduced planktonic cell propagation as expected. Our results offer new insights into the mechanical understanding of biofilm formation shaped by environmental stresses and associating biological responses.