Longitudinal assessment of oral probiotics on gut microbiota development and Eimeria infection in young forest musk deer

Abstract The forest musk deer (Moschus berezovskii), an endangered species in China, faces significant challenges in population recovery, particularly among young individuals in captivity, due to Eimeria infections. This study investigated the effects of oral supplementation with Lactobacillus plantarum P-8 and Lactobacillus casei Zhang on parasite infection, gut microbial succession, predicted microbiota maturity, and faecal immune markers. Twenty juveniles were randomly assigned to a control (CT) or probiotic (PB) group and monitored longitudinally across four developmental phases (hiding, conflict, maternal separation, and independent). Generalized linear mixed-effects models showed no significant effects of probiotic supplementation on Eimeria prevalence or oocyst counts. Gut microbial diversity and community composition changed markedly across developmental phases, whereas probiotic supplementation had no significant overall effect. A Random Forest-derived microbiota maturity model explained 46.56% of the variation in the response variable and indicated phase-specific differences in predicted microbiota maturity between treatment groups. Overall, host developmental stage was the primary factor associated with gut microbiota development, while probiotic supplementation was associated with modest, phase-specific differences without altering the overall successional trajectory. These findings provide insights into gut microbiota development and may inform microbiota-based management strategies for captive forest musk deer.