Community living causes changes in metabolic behavior and is permitted by specific growth conditions in two bacterial co-culture systems

Abstract

Although bacteria exist in complex microbial communities in the environment, their features and behavior are most often studied in monoculture. While environmental enrichments or complex co-cultures with tens or hundreds of members might more accurately represent the natural communities of bacteria, we sought to create simple pairs of organisms to learn what conditions create successful co-culture and how bacteria change transcriptionally when a partner species is present. We grew two pairs of organisms in co-culture, Pseudomonas aeruginosa and Escherichia coli and Lacticaseibacillus rhamnosus and Bacteroides thetaiotaomicron. At first, both co-cultures failed, with one organism outcompeting the other. However, through manipulating media and environmental conditions, we created co-cultures with stable member ratios over many generations for each community. We then show that changes in the expression of metabolic genes are present in all studied species, with key catabolic and anabolic pathways often upregulated in the presence of another organism. These changes in gene expression fail to occur in conditions that will not lead to successful co-culture, suggesting they are essential for adapting to and surviving in the presence of others.