Ecological succession and topological rewiring of the oral microbiome in giant panda cubs

Abstract In specialized herbivores retaining a carnivorous digestive tract, such as the giant panda, early-life oral microbiome assembly is crucial for lifelong health, yet remains poorly understood. Here, we longitudinally tracked the saliva and supragingival plaque microbiomes of captive cubs (180 matched samples) from birth to one year using microbiome sequencing and topological cartography. We demonstrate a profound spatial-temporal divergence driven by deterministic succession. Initial plaque colonization exhibited transient priority effects reflecting maternal imprints, rapidly superseded by autogenic niche reconstruction and deep anaerobic maturation. Host ontogeny, notably deciduous tooth eruption, triggered intense microbial exchange, causing significant transient habitat homogenization (peak Mantel correlations at months 6 and 8, p < 0.001). Mature plaque selectively enriched for peptidoglycan biosynthesis and complex carbohydrate degradation, establishing a pre-adaptive metabolic reservoir for the impending high-fiber bamboo diet. Crucially, topological analysis (interaction edges expanded 3.4-fold) revealed that early pioneers evade competitive exclusion by shifting their ecological niche to become inter-module connectors (Pi > 0.62), providing spatial scaffolds for late-arriving climax communities. These findings decipher the deterministic assembly rules of saliva and plaque microbiomes during the extreme milk-to-bamboo dietary transition, advancing our understanding of giant panda adaptive evolution and identifying native keystone targets for preventive veterinary interventions.