RNAseq of bacterial co-culture

Characterizing natural microbial communities remains a significant challenge due to the complexity of the metabolic networks formed between populations as cells compete for limited resources. Synthetic ecosystems are useful for dissecting and disentangling these interactions because the controlled conditions enable quantitative measures and modelling of interactions between community members. To identify and parameterize metabolic interactions between bacterial species, we established defined communities in which Escherichia coli was the only species able to access a sole carbon source, lactose, and Salmonella enterica was dependent on metabolic byproducts produced by E. coli. The S. enterica population producing colicin Ib can exploit E. coli by causing the release of beta-galactosidase into the culture medium, which in turn makes glucose and galactose available as common goods for community members. These dependencies and antagonistic interactions created a paradoxical relationship in which S. enterica depended on E. coli to produce carbon and energy nutrients while simultaneously threatening ecosystem stability by killing the primary producer. To assess the impact of bacteriocin (colicin Ib) impact on this cross-feeding community, we performed an RNAseq experiment on S. enterica and E. coli co-cultures. We used wildtype S. enterica and wildtype E. coli strains, S. enterica cib/imm mutant which does not produce colicin Ib, and E. coli cirA mutant which is immune to killing by colicin Ib.