Microbial communities can be incredibly useful, if only we could control their dynamics. Our lab is interested in controlling both ecological and evolutionary dynamics.
Using models, we have studied single species bioreactors containing a cooperative degrader (e.g. the bacteria need to produce an enzyme to break down a toxin that’s beneficial for all cells in the culture) and analysed whether we could control the emergence of mutants that cheat and no longer degrade the toxin [1]. We found that by varying the concentration of the medium inflow rates we could favour the invasion of cooperators into cheater populations, but eventually cheaters would always win. The only way to maintain cooperation is to periodically add them back into the bioreactor.
We have also worked on models to study how to control community stability in the context of a spatially organised system like the gut [2]. We modelled two compartments into which species can migrate from an outside pool, or from one compartment to the other (but not vice versa). In the context of the gut, this would represent microbial communities in two parts of the gastrointestinal tract, such as the mouth and the intestines. We could show that having such spatial structure stabilises the downstream community (the intestine in our example), especially if species in the upstream compartment have a positive effect on the species residing downstream.
More recently we have been studying community control experimentally in the lab. In one project, we are feeding an acidifying species embedded in a community to control the growth of a pathogen that is sensitive to low pH. In another project, we are altering medium composition in chemostats to control the coexistence of two strains that compete for a single carbon source.
References
1. S. Shibasaki, S. Mitri (2020) Evol Appl.
2. S. Shibasaki, S. Mitri (2023) iScience.