(312b) Amino Acid Cross-Feeding Enables Inter- and Intra-Species Cooperation (Industry Candidate)

Naturally occurring bacterial communities are able to cooperate to complete complex tasks by splitting these tasks between organisms and reducing the metabolic burden placed on each individual strain. The ability to distribute tasks and the metabolic load is of interest for biotechnology applications where dividing labor between populations can address bottlenecks in production and allow one to take advantage of the natural strengths of a specific strain. The potential benefits of creating synthetic communities capable of sharing metabolic load are challenged by the difficulty in co-culturing microbes. One way to combat this challenge is to use pairs of auxotrophic microbes. By growing two microbes with different auxotrophies in a nutrient deficient environment, the two microbes can trade essential nutrients, or cross-feed to enable the mutualistic growth of both organisms. To explore the use of cross-feeding we have assessed the growth of two industrially relevant bacterial hosts in both inter- and intra-species pairs of auxotrophs and examined transcriptomic profiles of successfully cross-feeding pairs.

We have quantified growth of 14 amino acid auxotrophs of E. coli and 6 amino acid auxotrophs of B. megaterium in both inter- and intra-species pairings. Cross-feeding success was evaluated in three different culture types: semi-solid agar plates, batch, and continuous culture. We observed that cross-feeding occurs both in both inter- and intra-species cross-feeding pairs of bacteria and identified pairs that cross-feed for inter- and intra-species pairs in all three culture types. Using this growth data we have identified two “super donors”, strains of both E. coli and B. megaterium that grow with many other amino acid auxotrophs in both inter- and intra-species pairs.

To characterize how the cells are responding to the co-culture environment and cross-feeding we generated gene expression profiles of three inter-species pairs of auxotrophs that cross-feed successfully in all three of our tested culture types. Supernatant and transcriptomic samples were taken from the cross-feeding pairs in continuous culture, as well as monocultures grown in a minimal media supplemented with their essential amino acid. The data generated via the transcriptomic analysis of the interspecies cross-feeders was used to assess how strains adapt to co-culture with an auxotrophic partner. Preliminary evaluation of differential gene expression between E. coli co-cultures and monocultures show that not all strains react the same to co-culture. We also found an upregulation of amino acid transporter and amino acid biosynthesis genes in co-cultured E. coli strains as compared to their monoculture counterparts. This work shows that using cross-feeding pairs of bacteria can enable us to build functional synthetic microbial communities by addressing the difficulties in co-culture growth.