From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process

Predicting and promoting gut microbiome recovery following perturbations such as antibiotic treatment, dietary shifts, or inflammation remain major challenges in microbiome science and clinical practice. In this review, we explore recent advances in microbiome restitution by framing recovery as a dynamic ecological process shaped by complex interactions between microbial taxa, host physiology and environmental conditions. We review current evidence addressing four key questions that outline the salient ecology of perturbation and recovery: which microbial taxa are present in the microbiota and which taxonomic or functional qualities might increase susceptibility to perturbation; what is the nature of the perturbation, including the type and probable targets of the perturbation, as well as the indirect ecological and environmental consequences of that perturbation; what is the time course of perturbation and recovery, exploring prehabilitation strategies and successional trajectories as a staged recovery framework; and where does perturbation and recovery unfold in the gut, with attention to both regional and microscale spatial patterns. Highlighting recent advances from multi-omics approaches and longitudinal studies, we demonstrate how each of these factors and their interactions critically shape both robustness to disturbance and the trajectory of recovery. We advocate for multimodal, context-specific interventions that harness ecological principles to drive regrowth and community assembly, including diet, targeted microbial transplantation and modulation of the abiotic gut environment. Ultimately, resolving the challenge of microbiome restitution will require personalized strategies informed by ecological understanding and longitudinal functional monitoring. This paradigm provides a foundation for future translational advances to promote eubiosis and improve patient outcomes in microbiome-related diseases.