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.

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The gut microbiome plays a vital role in human health. Disturbances of this microbial system is associated with diseases such as obesity and inflammatory bowel disease. In populations of microbial species, many organisms partake in byproduct cross-feeding interactions, where byproducts from one organism are consumed by other microbes. Using the digital evolution software Avida, I studied the effect of recurring perturbations and imperfect resource conversion on the evolution of byproduct cross-feeding chains in digital communities. To investigate the effect of perturbation and conversion rate on digital organisms, I evolved digital communities for 200,000 updates in an unperturbed environment that could hold 50 different resource types, each produced as a byproduct of consuming another resource. At 200,000 updates, 50 or 60 % of all organisms were removed at various intervals during periods of different lengths, with a conversion rate less than 100 % between resources in the byproduct chain. I found that 0.9 conversion rate caused communities to evolve longer cross-feeding chains. A conversion rate of 0.5 resulted in communities with much shorter chains, more similar in length to byproduct chains in the human gut. Perturbation events seem to affect chain length only under certain conditions when energy is lost between resources, for example when 60 % of all organisms were removed every 50th update on average. It appears that conversion loss makes digital communities more robust against the effects of perturbations, and that it might protect these communities from going extinct.

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.