Partitioning the roots of interactions between microbes (PRISM): environment-supplied resources versus species-produced mediators

Microbial species in a community can interact through competition for resources present in the environment, as well as inhibition or facilitation by metabolites produced by other species. Understanding the relative contribution of these two types of interaction will help us modulate bacterial interactions more effectively. Our work focuses on partitioning the impact of metabolites that mediate the interactions between bacteria into the contribution of resources present in the environment versus that of mediators released as by-products of cellular activities. For this, we create a range of conditions in which the ratio of environmentally supplied resources (R) and the species-produced metabolites (M) is modulated to infer the contribution of each to the overall interaction. We performed this assay with six different nasal bacterial strains and saw an array of outcomes in terms of how secreted metabolites by one strain affected other nasal strains. Metabolites produced by Staphylococcus suppressed the growth of most strains tested. In contrast, metabolites produced by commensal strains such as Corynebacterium accolens and Corynebacterium tuberculostearicum could aid the growth of Staphylococcus aureus and Staphylococcus epidermidis strains. Interestingly, the growth of Staphylococcus epidermidis benefited from metabolites produced by four out of the five strains tested. Our proposed assay offers additional insights into the roots of bacterial interactions, enabling applications such as engrafting helpful probiotics and knocking out harmful bacteria.