The human gut microbiome is a complex ecosystem with hundreds of species interacting with each other and the host. One function of the microbiome is to break down undigested nutrients into smaller nutrients, sometimes available for uptake by the host. The digestion of such macromolecules can involve several species where one feeds on another’s byproducts, forming a large cross-feeding network. The method of digital evolution can be of great aid in studying such complex ecosystems by creating models of the studied system. In this study, the digital evolution software Avida was used to study the effects of perturbations in the system on byproduct cross-feeding chain length. Intense perturbations were found to shorten the chain lengths in general whereas weaker perturbations had either a small or no effect. When perturbations ceased, most byproduct chains displayed recovery to lengths similar to the preperturbation lengths. This indicates that byproduct chain lengths may be kept short by common ecological mechanisms alone, explaining why very long chains are rarely observed while still theoretically possible.