<p>This paper deals with the computational modelling of the bioluminescence pattern formation in suspensions of luminous <i>Escherichia coli</i> bacteria. The aim of this work is to improve the reaction–diffusion–chemotaxis model by introducing modulation functions applied to the rates of the bacterial growth, the chemoattractant production and the oxygen consumption as well as to investigate the influence of the function form on the spatiotemporal pattern formation in an <i>E. coli</i> colony. The nonlinear two-dimensional-in-space model was used to simulate the pattern formation in aqueous cultures of bacteria along the inner lateral surface and along the three-phase contact line of a cylindrical micro-container. The simulated patterns are analysed in order to determine the form of the modulation functions and values of the model parameters closely matching patterns experimentally observed in a luminous <i>E. coli</i> colony. A linear stability analysis of the corresponding one-dimensional-in-space model is applied to determine values of the parameters triggering the self-organisation of the bacterial colony. The numerical simulation at the transient conditions was carried out using the finite difference technique.</p>