Microbial Variability in Zoo-Housed Alaotran Gentle Lemurs: Host-Associated Factors and Environmental Influences

Primates worldwide face escalating ecological pressures, driving many species to rapid declines. Modern zoos play an essential role by maintaining viable populations and improving welfare through research-driven management. However, gut-microbiome interactions in captive primates remain poorly understood. Our study investigated how host-specific traits influence fecal microbiota composition, whether shared environments facilitate shared microbial signatures, and whether fluctuations in fecal cortisol and testosterone correspond to microbial changes. We also evaluated the combined use of hormonal and microbiota analyses as a noninvasive tool to support welfare and health monitoring in zoo-housed Hapalemur alaotrensis. We monitored 4 groups (n = 8) housed across 4 European facilities, yielding 180 fecal samples across 3 collection phases. We characterized microbial communities through 16S rRNA gene sequencing following DNA extraction and quality checks, and quantified hormone metabolites using ELISA kits. We performed statistical analyses to evaluate the effects of facility, collection phase, and host-specific traits on microbiota composition and hormone concentrations. Microbiota profiling revealed diverse bacterial communities, with facility-associated differences representing the strongest and most consistent pattern, while effects of sex and scent enrichment were weak and inconsistent. Hormone concentrations did not vary across collection phases, although cortisol differed among facilities. No significant associations between hormone concentrations and microbiota profiles were detected. Given the small sample size, these findings should be considered exploratory, providing initial evidence of facility-associated microbiome variation in zoo-housed H. alaotrensis. Larger studies are needed to investigate its potential drivers and evaluate whether combined microbiome and endocrine assessments may contribute to primate welfare monitoring.