title: An individual-based modeling approach to simulate the effects of cellular nutrient competition on Escherichia coli K-12 MG1655 colony behavior and interactions in aerobic structured food systems.
abstract: Traditional kinetic models in predictive microbiology reliably predict macroscopic dynamics of planktonically-growing cell cultures in homogeneous liquid food systems. However, most food products have a semi-solid structure, where microorganisms grow locally in colonies. Individual colony cells exhibit strongly different and non-normally distributed behavior due to local nutrient competition. As a result, traditional models considering average population behavior in a homogeneous system do not describe colony dynamics in full detail. To incorporate local resource competition and individual cell differences, an individual-based modeling approach has been applied to Escherichia coli K-12 MG1655 colonies, considering the microbial cell as modeling unit. The first contribution of this individual-based model is to describe single colony growth under nutrient-deprived conditions. More specifically, the linear and stationary phase in the evolution of the colony radius, the evolution from a disk-like to branching morphology, and the emergence of a starvation zone in the colony center are simulated and compared to available experimental data. These phenomena occur earlier at more severe nutrient depletion conditions, i.e., at lower nutrient diffusivity and initial nutrient concentration in the medium. Furthermore, intercolony interactions have been simulated. Higher inoculum densities lead to stronger intercolony interactions, such as colony merging and smaller colony sizes, due to nutrient competition. This individual-based model contributes to the elucidation of characteristic experimentally observed colony behavior from mechanistic information about cellular physiology and interactions.
authors.affiliation: BioTeC - Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 Box 2423, B-3001 Leuven, Belgium. Electronic address: ignace.tack@cit.kuleuven.be.
authors.forename: Ignace L M M
authors.initials: IL
authors.lastname: Tack
authors.affiliation: BioTeC - Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 Box 2423, B-3001 Leuven, Belgium. Electronic address: filip.logist@cit.kuleuven.be.
authors.forename: Filip
authors.initials: F
authors.lastname: Logist
authors.affiliation: BioTeC - Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 Box 2423, B-3001 Leuven, Belgium. Electronic address: estefania.noriegafernandez@cit.kuleuven.be.
authors.forename: Estefanía
authors.initials: E
authors.lastname: Noriega Fernández
authors.affiliation: BioTeC - Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 Box 2423, B-3001 Leuven, Belgium. Electronic address: jan.vanimpe@cit.kuleuven.be.
authors.forename: Jan F M
authors.initials: JF
authors.lastname: Van Impe
mesh_terms: D000332:Aerobiosis; D048168:Escherichia coli K12 / Q000737:chemistry / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D005504:Food Analysis; D005516:Food Microbiology; D008962:Models, Theoretical
keywords: Individual-based modeling; Microbial colony dynamics; Microbial intracolony and intercolony interactions; Predictive microbiology; Repast Simphony; Structured food model systems