Individual-based modelling (IbM) in food microbiology: A comprehensive guideline

Abstract

Individual-based modelling (IbM) presents opportunities to help us understand the dynamics of the food microbial ecosystem. Yet, IbM is generally perceived as a difficult and specialized modelling tool that is not fully fledged for food microbiology-particularly in terms of scalability, computational efficiency, and ease of integration with existing models. This guideline aims to demystify IbM and demonstrate its practical applications in food microbiology. We present a structured 5D protocol (Define, Dissect, Develop, Deploy, and Demonstrate) to guide the design and implementation of IbM. To support practical adoption, we provide a detailed case study that simulates the growth of an E. coli K-12 MG1655 monolayer colony in a homogeneous gel medium under aerobic conditions. A review of existing IbM toolkits is also included to highlight their relevance and application in modelling food-related microbial dynamics.

Keywords: Individual interactions; Individual variability; Individual-based modelling (IbM); Predictive food microbiology; Spatial heterogeneity.