Temporal dynamics of human gut microbiota revealed by the “Lunar Palace 365” experiment

With the advancement of crewed deep space exploration, maintaining microbiome health in long-term confined environments is crucial for life support systems. The gut microbiota, a complex ecosystem, shows stability and multiple stable states, but its ecological succession and stability in bioregenerative life support systems (BLSS) remain poorly understood. This study, based on the "Lunar Palace 365″ experiment, analyzed 376 fecal samples from eight crew members across three mission phases. By combining metagenomic sequencing with clustering based on the Jensen-Shannon distance, we reconstructed dynamic trajectories of gut microbial communities, identified stable state configurations, and evaluated responses to environmental perturbations such as simulated window blackouts and power outages. Despite highly controlled conditions, the gut microbiota exhibited pronounced interindividual variability and multiple stable configurations, with phase dependent and individual specific temporal patterns observed across taxa. Environmental perturbations significantly altered microbial stable states and triggered delayed recovery, suggesting an “ecological memory” mechanism. This study defines the succession patterns and stability of the gut microbiota in BLSS, highlights host associated influences, and provides a foundation for microbiome health strategies in future space missions.