Fecal Microbiomes in Ex Situ-Managed Mammals: Captivity-Associated Shifts and Links to Welfare, Stress, and Reproductive Performance

Ex situ conservation programs maintain threatened mammal populations and support conservation breeding and reintroduction, but success also depends on physiological function, behavioral competence, welfare, and reproductive performance. This critical narrative review combined structured literature searches with a descriptive quantitative evidence map of published summary values to evaluate mammalian fecal or intestinal microbiomes in relation to wild–captive transitions, diet and management, welfare-related outcomes, and reproduction. Captivity was repeatedly associated with altered microbial community composition, but richness and major phylum-level changes showed no universal direction. Host phylogeny, diet, digestive anatomy, facility, environmental exposure, reproductive state, and analytical methods constrained comparisons. Five studies provided direct Tier 1 evidence by jointly measuring microbiomes with outcomes spanning stereotypic behavior, stress and endocrine measures, breeding season, breeding success, and multigenerational fitness within the same ex situ-managed populations. These included associations with stereotypic behavior, breeding season, hormone metabolites, breeding success, and multigenerational fitness trajectories. However, the evidence remains observational and taxon-specific, and no bacterial feature is currently validated as a transferable biomarker. Longitudinal fecal microbiome monitoring may add value when integrated with behavioral, endocrine, clinical, dietary, and breeding data. Standardized repeated-measures studies, functional profiling, and prospective management interventions are priorities for translating microbiome research into evidence-based ex situ conservation.