Abstract
Understanding gut microbiome diversity in endangered chimpanzees (Pan troglodytes) is crucial for their effective ex situ conservation. This study characterized the age-related dynamics of the fecal microbiota in captive juvenile (< 5 years), adolescent (5–10 years), and adult (> 15 years) chimpanzees reared in Shanghai and Hangzhou Zoos using 16S rRNA sequencing and demonstrated significant ontogenetic shifts in the microbiota composition. Alpha diversity peaked in adolescents (significantly higher Ace/Chao1/Observed Species; p < 0.05), with the greatest number of unique OTUs (1,139). Community structures significantly differed between the age groups (ANOSIM R = 0.121). Furthermore, the captive diets drove the fundamental restructuring of the core phyla. The Firmicutes/Bacteroidetes ratio was considerably lower in captive individuals than in wild conspecifics. The discriminative taxa were also analyzed. Notably, the abundance of Lactobacillus increased significantly in adults (5.44% ± 4.43%) compared to younger groups (< 1.26%), whereas that of Prevotella decreased with age. These findings demonstrate the regulatory role of age in determining gut microbiome in captivity, which is potentially attributed to physiological transitions and dietary adaptations, which present a basis for microbiome-informed health monitoring and age-specific dietary management for the welfare of captive chimpanzees.