Predicting partner fitness based on spatial structuring in a light-driven microbial community
Authors: Sakkos Jonathan K. , Santos-Merino María , Kokarakis Emmanuel J. , Li Bowen , Fuentes-Cabrera Miguel , Zuliani Paolo , Ducat Daniel C. 
Published: October 2022

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology (e.g., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

Author Summary

Microbial communities, play important, yet poorly understood roles in health and agriculture. As we develop a better understanding of how these communities interact together, as well as with their host organisms, there is growing interest in engineering communities with specific functions, such as for treating disease, personalized probiotics, or aiding plants with nutrient uptake. To better understand how these microbes interact with each other, we want to monitor the exchange of metabolites and the locations of the microbes, tasks which at present are technically challenging, if not impossible. Where experimental approaches for monitoring metabolites are limited, computational tools can enable greater access to the fate of both chemicals and microbes within a community. In this study, we developed a computerized model of a synthetic microbial community of two bacteria, one which performs photosynthesis and supplies sugar and another which consumes the sugar for growth. We showed that the relative level of sugar secretion regulates not only the steady-state support for the consumer partner’s growth, but also how the community changes with time. To determine the importance of spatial organization within the community, we fit a model and used it to predict colony growth. We anticipate that the synergy between experimental and computational approaches will improve our ability to design microbial communities with new functions.