Automated design of synthetic microbial communities

Microbial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between species diversity and productivity of communities. The pervasiveness of these communities in nature highlights possible advantages for genetically engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially as functional complexity increases. Here, we demonstrate a methodology for designing robust synthetic communities that include competition for nutrients, and use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We computationally explore all two- and three- strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and further tuning the community composition. In naturally occurring microbial systems, there is a positive relationship between species diversity and productivity of the community. Here the authors perform model selection to find potential amensal interactions that yield robust stable synthetic microbial consortia.

Automated summary

In naturally occurring microbial systems, there is a positive relationship between species diversity and community productivity; researchers performed model selection to discover potential amensal interactions that lead to robust stable synthetic microbial consortia.