Individual variation within parasite communities of endangered African lions

Prey depletion and human-wildlife conflict threaten the critically endangered West African populations of lion (<i>Panthera leo leo</i>), which occupy less than 1.1% of their historic range in West Africa. These threats may alter behaviour through prey selection and affect exposure to parasites to compromise their health. We extracted DNA from faecal samples collected in four national parks in Benin, Burkina Faso and Senegal to characterize haemoparasites, nemabiome and microbiome. We used microsatellite markers to differentiate individuals and five primer sets to complete molecular analyses. From 20 individuals (12 males and 8 females), we found significant differences in the species richness and composition for all parasite groups across host populations and individual lions. We detected haemoparasites, including <i>Babesia</i> and <i>Sarcocystis</i> species, along with <i>Blechomonas</i>, a kinetoplastid, all of which raise potential health concerns. The nemabiome was dominated by <i>Ancylostoma</i> species (hookworms) with additional detections of lungworms from the genera <i>Oslerus</i> and <i>Troglostrongylus</i>. Significant interactions were found between population-level microbiome richness and both nemabiome and haemoparasite diversity. Our study provides the first effort to determine the parasite diversity among West African lion populations using non-invasive metabarcoding. Our findings highlight metabarcoding as a powerful tool to assess spatial variation in health and parasite diversity metrics for an endangered apex predator.