Modelling interactions that determine core gut microbiome stability to predict microbiome perturbation by opportunistic pathogens

The gut microbiome plays a crucial role in host homeostasis, with implications for nutrition, immune development, metabolism, and protection against pathogens. Changes in microbiome composition are associated with host health and after microbial shifts, opportunistic pathogens have a unique chance to invade and overgrow the microbiome However, the complexity of the microbiome inhibits understanding of cause and consequence. This study describes a species interaction model to predict gut microbiome stability. This method aids in understanding perturbation of the gut microbiome by opportunistic pathogens Escherichia coli and Bacteroides ovatus and validate predictions in co-culture growth experiments. Despite their inherent differences in growth rates and interaction with gut commensals, both E. coli and B. ovatus can successfully invade an established consortium. However, the mechanisms of invasion differ; B. ovatus replaces an original consortium bacterium, whereas E. coli integrates into the established microbiome. This research enhances our understanding of microbial invasion processes and their implications for gut microbiome stability and host health.