Bioprinting microbial communities to examine interspecies interactions in time and space

Abstract

Bioprinting experiments have emerged as an approach for studying complex cellular interactions in the context of spatial structure, ranging from intracellular networks to interspecies interactions in communities. Despite the progress made in developing and optimizing computational modeling parameters to recapitulate these interactions in silico, experimental verification of model predictions in vitro is often elusive, due to the limits of common laboratory culturing methods, especially at the micro- and nanoscale. In this work, micro-scale bioprinting was used to evaluate the spatiotemporal effects of metabolite sharing between partners in an artificial syntrophic consortium consisting of Salmonella enterica serovar Typhimurium and Escherichia coli. Micro-colonies of these bacteria were patterned at increasing spatial separation distances, in the presence of competitor or cooperator strains. Growth of the consortium members was evaluated and compared to predictions generated by a bacterial growth modeling platform known as Computation of Microbial Ecosystems in Time and Space (COMETS). In close agreement with simulation, experimental metabolite sharing between micro-colonies exhibited strong distance-dependency. When bioprinted micro-colonies were confronted with one-way or two-way diffusion barriers, such as the intervention of cooperative or competitive bacteria, experimental results showed that spatial positioning of the barriers critically influences metabolite sharing between consortium members. These results were generally predicted by simulation in COMETS. Our results demonstrate the utility of micro-scale bioprinting to experimentally test which aspects of predictive microbial growth models hold at this spatial scale, and for a range of synthetic biology applications.