Microbial Memory of Initial States Sustains Diversity and Resilience through Oscillatory Dynamics in Gut Microbiota

High bacterial diversity is crucial for maintaining gut microbiota (GM) functions like digestion, nutrient absorption, and resilience to disruptions. Paradoxically, despite limited substrates in the human intestinal tract (HIT) and intense interspecies competition that should reduce diversity, GM sustains remarkable species richness and stability. This study investigates how memory for initial states (MFIS)—a bacterial capability to retain and respond to initial population levels—enables this diversity and resilience. We combined in vitro experiments (Bacteroides vulgatus, Bifidobacterium longum, and Lactobacillus acidophilus isolated from athletes and enteritis patients) with fractional-order kinetic modeling (FOKM) and simulations. Results revealed that strong MFIS (prominent in athletes’ GM) drives periodic population oscillations, reducing competition and enabling stable, diverse communities. Conversely, weak MFIS (in patients’ GM) led to competitive exclusion and low diversity. Critically, MFIS facilitated closed-loop regulation, allowing GM to rebound from environmental perturbations by restoring initial states. This work lays a theoretical basis for understanding of the ecological effect of MFIS on formation and maintenance of bacterial diversity in GM as well as its high ecological resilience to environmental perturbations.