Modulating microbial intake helps to maintain the gut microbiome diversity

The animal gut is home to a myriad of microbes whose diversity has a proven impact on the host's health. Indeed, lower values of this metric often correlate with pathological status. In this context, processes involved in the gut microbiome assembly have been studied in the search for optimal nutritional habits and medical interventions. While the nutritional content of food has been extensively investigated, its microbial content has comparatively received little attention as an ecological driver of the gut microbiome. Furthermore, while probiotics use is increasing, the question of optimal dose remains open. Here, we fill these gaps by designing a model that tracks the effect of microbial migration bursts - that result from feeding and/or from probiotics administration - on the gut community alpha-diversity. We find that there is a set of feeding parameters (feeding interval and food microbial content) that maximizes the gut Shannon alpha-diversity, which we call the Maximal Diversity Strategy (MDS). Using a combination of numerical and analytical techniques, we show that for large numbers of microbial types, in the diversity maximization scenario, diversity converges to that of the food, and the feeding rate converges to the average clearance rate. These results remain robust both to the choice of distribution for the parameters that describe microbial dynamics and to weak dispersal noise, thus increasing their theoretical significance and potential for empirical exploration. We believe this work can help evaluate how quantitative ecological control can be used to improve the intake protocols of live biotherapeutic products.