Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections. The multifactorial nature of biofilm development and drug tolerance imposes great challenges for the use of conventional antimicrobials and indicates the need for multi-targeted or combinatorial therapies. In this Review, we focus on current therapeutic strategies and those under development that target vital structural and functional traits of microbial biofilms and drug tolerance mechanisms, including the extracellular matrix and dormant cells. We emphasize strategies that are supported by in vivo or ex vivo studies, highlight emerging biofilm-targeting technologies and provide a rationale for multi-targeted therapies aimed at disrupting the complex biofilm microenvironment.

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Targeting microbial biofilms: current and prospective therapeutic strategies.

SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.

https://tandfonline.com/doi/pdf/10.1080/1040841X.2016.1208146

Critical review on biofilm methods

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments.

https://www.zora.uzh.ch/id/eprint/194894/1/24_OA_1_2020_Karygianni_TrendsMicrobiol.pdf

Biofilm Matrixome: Extracellular Components in Structured Microbial Communities

We summarize different studies describing mechanisms through which bacteria in a biofilm mode of growth resist mechanical and chemical challenges. Acknowledging previous microscopic work describing voids and channels in biofilms that govern a biofilms response to such challenges, we advocate a more quantitative approach that builds on the relation between structure and composition of materials with their viscoelastic properties. Biofilms possess features of both viscoelastic solids and liquids, like skin or blood, and stress relaxation of biofilms has been found to be a corollary of their structure and composition, including the EPS matrix and bacterial interactions. Review of the literature on viscoelastic properties of biofilms in ancient and modern environments as well as of infectious biofilms reveals that the viscoelastic properties of a biofilm relate with antimicrobial penetration in a biofilm. In addition, also the removal of biofilm from surfaces appears governed by the viscoelasticity of a biofilm. Herewith, it is established that the viscoelasticity of biofilms, as a corollary of structure and composition, performs a role in their protection against mechanical and chemical challenges. Pathways are discussed to make biofilms more susceptible to antimicrobials by intervening with their viscoelasticity, as a quantifiable expression of their structure and composition.

https://pure.rug.nl/ws/files/16231894/femsre.fuu008.full.pdf

Viscoelasticity of biofilms and their recalcitrance to mechanical and chemical challenges

Conditions of lateral surface confinement that promote tissue-cell integration and inhibit biofilm growth

Bacterial adhesion is problematic in many diverse applications. Coatings of hydrophilic polymer chains in a brush configuration reduce bacterial adhesion by orders of magnitude, but not to zero. Here, the mechanism by which polymer-brush functionalized surfaces reduce bacterial adhesion from a flowing carrier fluid by relating bacterial adhesion with normally oriented adhesion and friction forces on polymer (PEG)-brush coatings of different softness is studied. Softer brush coatings deform more than rigid ones, which yields extensive bond-maturation and strong, normally oriented adhesion forces, accompanied by irreversible adhesion of bacteria. On rigid brushes, normally oriented adhesion forces remain small, allowing desorption and accordingly lower numbers of adhering bacteria result. Friction forces, generated by fluid flow and normally oriented adhesion forces, are required to oppose fluid shear forces and cause immobile adhesion. Summarizing, inclusion of friction forces and substratum softness provides a more complete mechanism of bacterial adhesion from flowing carrier fluids than available hitherto.

Normally Oriented Adhesion versus Friction Forces in Bacterial Adhesion to Polymer-Brush Functionalized Surfaces Under Fluid Flow

Traditionally biomaterials development consists of designing a surface and testing its properties experimentally. This trial-and-error approach is limited because of the resources and time needed to sample a representative number of configurations in a combinatorially complex scenario. Therefore, computational modeling is of significant importance in identifying best antibacterial materials to prevent and treat implant related biofilm infections. In this paper we focus on bifunctional surface with polymer brushes and Pluronic-Lysozyme conjugates developed by Henk Busscher's group in Groningen, The Netherlands. The bifunctional brushes act as anti-adhesive due to the unmodified polymer brushes and antibacterial, because of the Pluronic-Lysozyme conjugates. They developed and studied three different surfaces with varying proportions of antibacterial and anti-adhesive properties. In order to aid the development of optimal bifunctional surfaces, we build a three dimensional computational model using BioScape, an agent-based modeling and simulation language developed by Compagnoni's group at Stevens. We model two different experimental phases: adhesion and growth. We use the results of experiments on two surfaces as training data, and we validate our model by reproducing the experimental results from the third surface. The resulting model is able to simulate varying configurations of surface coatings both at adhesion and growth phases at a fraction of the time necessary to perform in-vitro experiments. The output of the model not only plots populations over time, but it also produces 3D-rendered videos of bacteria-surface interactions enhancing the visualization of the system's behavior.

Henny C. van der Mei

Papers

Viscoelasticity of biofilms and their recalcitrance to mechanical and chemical challenges

Conditions of lateral surface confinement that promote tissue-cell integration and inhibit biofilm growth

Normally Oriented Adhesion versus Friction Forces in Bacterial Adhesion to Polymer-Brush Functionalized Surfaces Under Fluid Flow

Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape