Recurring perturbations limit the length of byproduct cross-feeding chains in digital communities

The human gut microbiome is important for health and development, and understanding its functioning and dynamics are of great medical importance. The microbiome food web is largely characterized by chains of byproduct cross-feeding (where metabolites of one organism are used as nutrients for another), yet a recent study have shown that the average length of the chains are considerably shorter than what metabolic capabilities of present species allow for. Here, I use evolving populations of digital organisms to investigate if recurring perturbations are a potential constraint of byproduct cross-feeding chains. I evolved digital populations in an environment unconstrained by energy loss between trophic levels and then exposed them to a period of recurring perturbations, where a fraction of the population was removed at 100 random points in time. Perturbations caused a substantial decrease in cross-feeding chain length, with increased frequency as perturbation intensity increased. In some communities, effects persisted after the perturbation period had ended. Tracking evolution of resource use during and after the perturbation period revealed that organisms descending from long-chained ancestors often evolved a shorter chain, suggesting that they adapted to perturbations by losing the ability to consume low-level resources. The evolutionary loss of resource consumption could explain the persisting effects on cross-feeding chains. Though my study suggests that perturbations can limit the length of byproduct cross-feeding chains, further studies are necessary toconclude if effects remain in environments with a more realistic energy transfer between trophic levels.