Abstract
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.
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Data availability
The computationally generated data used in this work is available at Zenodo https://doi.org/10.5281/zenodo.18802496106.
Code availability
The computer codes used in this work are available at Zenodo https://doi.org/10.5281/zenodo.18802496106.
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Marquioni, V. M., Hofacker, A.-C., Villavicencio, J. V. & Bansept, F. Code and data for the Paper: “Modulating microbial intake helps to maintain the gut microbiome diversity.” https://doi.org/10.5281/zenodo.18802496 (2026).
Acknowledgements
We thank members of the M3G group for insightful discussions, especially Florian Labourel. We thank Brendan Bohannan, Raghuveer Parthasarathy, and Kayla C. Evens for valuable help with zebrafish data. The project leading to this publication has received funding from France 2030, the French Government program managed by the French National Research Agency (ANR-16-CONV-0001), and from Excellence Initiative of Aix-Marseille University – A*MIDEX. FB thanks Román Zapién-Campos, Ana Teles, and Thomas Roeder for discussions that led to the onset of the project.
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F.B. conceived the project, A.-C.H. and J.V.V. worked on an earlier version of the model. V.M.M. extended the original model, performed the numerical and analytical study, and analyzed the results. VMM wrote the original draft, V.M.M. and F.B. edited it. All authors approved the final version of the manuscript.
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Marquioni, V.M., Hofacker, AC., Villavicencio, J.V. et al. Modulating microbial intake helps to maintain the gut microbiome diversity.
Commun Biol (2026). https://doi.org/10.1038/s42003-026-09867-6
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DOI: https://doi.org/10.1038/s42003-026-09867-6
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