Diffusive transport through a model host-biofilm system

The non-attached biofilm aggregate

Biofilms have conventionally been perceived as dense bacterial masses on surfaces, following the five-step model of development. Initial biofilm research focused on surface-attached formations, but detached aggregates have received increasing attention in the past decade due to their pivotal role in chronic infections. Understanding their nature sparked fervent discussions in biofilm conferences and scientific literature. This review consolidates current insights on non-attached aggregates, offering examples of their occurrence in nature and diseases. We discuss their formation and dispersion mechanisms, resilience to antibiotics and immune-responses, drawing parallels to surface-attached biofilms. Moreover, we outline available in vitro models for studying non-attached aggregates.

Diffusion of antibiotics through a biofilm in the presence of diffusion and absorption barriers

We propose a model of antibiotic diffusion through a bacterial biofilm when diffusion and/or absorption barriers develop in the biofilm. The idea of this model is: We deduce details of the diffusion process in a medium in which direct experimental study is difficult, based on probing diffusion in external regions. Since a biofilm has a gel-like consistency, we suppose that subdiffusion of particles in the biofilm may occur. To describe this process we use a fractional subdiffusion-absorption equation with an adjustable anomalous diffusion exponent. The boundary conditions at the boundaries of the biofilm are derived by means of a particle random walk model on a discrete lattice leading to an expression involving a fractional time derivative. We show that the temporal evolution of the total amount of substance that has diffused through the biofilm explicitly depends on whether there is antibiotic absorption in the biofilm. This fact is used to experimentally check for antibiotic absorption in the biofilm and if subdiffusion and absorption parameters of the biofilm change over time. We propose a four-stage model of antibiotic diffusion in biofilm based on the following physical characteristics: whether there is absorption of the antibiotic in the biofilm and whether all biofilm parameters remain unchanged over time. The biological interpretation of the stages, in particular their relation with the bacterial defense mechanisms, is discussed. Theoretical results are compared with empirical results of ciprofloxacin diffusion through Pseudomonas aeruginosa biofilm, and ciprofloxacin and gentamicin diffusion through Proteus mirabilis biofilm.

Hypoxia arising from concerted oxygen consumption by neutrophils and microorganisms in biofilms

Infections associated with microbial biofilms are often found to involve hypoxic or anoxic conditions within the biofilm or its vicinity. To shed light on the phenomenon of local oxygen depletion, mathematical reaction-diffusion models were derived that integrated the two principal oxygen sinks, microbial respiration and neutrophil consumption. Three simple one-dimensional problems were analyzed approximating biofilm near an air interface as in a dermal wound or mucus layer, biofilm on an implanted medical device, or biofilm aggregates dispersed in mucus or tissue. In all three geometries considered, hypoxia at the biofilm-neutrophil interface or within the biofilm was predicted for a subset of plausible parameter values. The finding that oxygen concentration at the biofilm-neutrophil juncture can be diminished to hypoxic levels is biologically relevant because oxygen depletion will reduce neutrophil killing ability. The finding that hypoxia can readily establish in the interior of the biofilm is biologically relevant because this change will alter microbial metabolism and persistence.

A new method to measure and model dynamic oxygen microdistributions in moving biofilms

Biofilms in natural environments offer a superior solution to mitigate water pollution. Artificially intensified biofilm reactors represented by rotating biological contactors (RBCs) are widely applied and studied. Understanding the oxygen transfer process in biofilms is an important aspect of these studies, and describing this process in moving biofilms (such as biofilms in RBCs) is a particular challenge. Oxygen transfer in RBCs behaves differently than in other biological reactors due to the special oxygen supply mode that results from alternate exposure of the biofilm to wastewater and air. The study of oxygen transfer in biofilms is indispensable for understanding biodegradation in RBCs. However, the mechanisms are still not well known due to a lack of effective tools to dynamically analyze oxygen diffusion, reaction, and microdistribution in biofilms. A new experimental device, the Oxygen Transfer Modeling Device (OTMD), was designed and manufactured for this purpose, and a mathematical model was developed to model oxygen transfer in biofilm produced by an RBC. This device allowed the simulation of the local environment around the biofilm during normal RBC operation, and oxygen concentrations varying with time and depth in biofilm were measured using an oxygen microelectrode. The experimental data conformed well to the model description, indicating that the OTMD and the model were stable and reliable. Moreover, the OTMD offered a flexible approach to study the impact of a single-factor on oxygen transfer in moving biofilms. In situ environment of biofilm in an RBC was simulated, and dynamic oxygen microdistributions in the biofilm were measured and well fitted to the built model description.

Continuum and discrete approach in modeling biofilm development and structure: a review

The scientific community has recognized that almost 99% of the microbial life on earth is represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and human activities, extensive experimental activity has been carried out to understand how biofilms grow and interact with the environment. Many mathematical models have also been developed to simulate and elucidate the main processes characterizing the biofilm growth. Two main mathematical approaches for biomass representation can be distinguished: continuum and discrete. This review is aimed at exploring the main characteristics of each approach. Continuum models can simulate the biofilm processes in a quantitative and deterministic way. However, they require a multidimensional formulation to take into account the biofilm spatial heterogeneity, which makes the models quite complicated, requiring significant computational effort. Discrete models are more recent and can represent the typical multidimensional structural heterogeneity of biofilm reflecting the experimental expectations, but they generate computational results including elements of randomness and introduce stochastic effects into the solutions.

Gel-Entrapped Staphylococcus aureus Bacteria as Models of Biofilm Infection Exhibit Growth in Dense Aggregates, Oxygen Limitation, Antibiotic Tolerance, and Heterogeneous Gene Expression

An experimental model that mimicked the structure and characteristics of in vivo biofilm infections, such as those occurring in the lung or in dermal wounds where no biomaterial surface is present, was developed. In these infections, microbial biofilm forms as cell aggregates interspersed in a layer of mucus or host matrix material. This structure was modeled by filling glass capillary tubes with an agarose gel that had been seeded with Staphylococcus aureus bacteria and then incubating the gel biofilm in medium for up to 30 h. Confocal microscopy showed that the bacteria formed in discrete pockets distributed throughout the gel matrix. These aggregates enlarged over time and also developed a size gradient, with the clusters being larger near the nutrient- and oxygen-supplied interface and smaller at greater depths. Bacteria entrapped in gels for 24 h grew slowly (specific growth rate, 0.06 h(-1)) and were much less susceptible to oxacillin, minocycline, or ciprofloxacin than planktonic cells. Microelectrode measurements showed that the oxygen concentration decreased with depth into the gel biofilm, falling to values less than 3% of air saturation at depths of 500 μm. An anaerobiosis-responsive green fluorescent protein reporter gene for lactate dehydrogenase was induced in the region of the gel where the measured oxygen concentrations were low, confirming biologically relevant hypoxia. These results show that the gel biofilm model captures key features of biofilm infection in mucus or compromised tissue: formation of dense, distinct aggregates, reduced specific growth rates, local hypoxia, and antibiotic tolerance.