Research into the control and optimization of natural and synthetic microbial communities has largely followed separate theoretical vs. experimental lines of inquiry. Both theory and experiments are valuable, but they are susceptible to modus operandi that may limit their correspondence and their translation to real world systems. Theoretical approaches typically adopt the analytical tractability of steady state dynamics, where microbes and the resources on which they depend are assumed to establish a stable equilibrium. In contrast, experimental approaches usually embrace the efficiency of serial-batch culture, where both the consumers and resources are made to fluctuate over several orders of magnitude with each passage.
We used simulations of a classic consumer-resource model to explore how the composition of communities varies under the steady-state conditions typically assumed by theory and the serially pulsed resource conditions routinely implemented experimentally. We found that overlap in community composition under continuous vs. pulsed resource supply decays rapidly with increasingly large intervals between resource replenishment, and that in the presence of a metabolically expected trade-off there is almost zero overlap in composition once the pulsing interval stretches beyond just four hours.
The implications for the growing field of microbial community optimisation is that it is essential the resource supply regime is tailored to the community being optimized. As such, we suggest that resource supply dynamics should be considered both a constraint in the design of novel microbial communities, and as a tuning mechanism for the optimization of pre-existing communities like those found in our own gut.