Modelling microbial communities using biochemical resource allocation analysis

Abstract

To understand the functioning and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, a large chasm between ecologically motivated descriptions of microbial growth used in many current ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed in the context of systems and synthetic biology. Here, we seek to demonstrate how resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parametrization. In particular, recent work on quantitative resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. These models go beyond Michaelis–Menten and Monod-type growth models, and are capable of accounting for emergent properties that underlie the remarkable plasticity of microbial growth. We outline the utility and advantages of using biochemical resource allocation models by considering a coarse-grained model of cyanobacterial growth and demonstrate how the model allows us to address specific questions of relevance for the simulation of marine microbial ecosystems, including the physiological acclimation of protein expression to different environments, the description of co-limitation by several nutrients and the differential use of alternative nutrient sources, as well as the description of metabolic diversity based on our increasing knowledge about quantitative cell physiology.