Nemabiome of roe deer and sheep living in sympatry

The growth of livestock farming and the recent expansion of wild ungulate populations in Europe favor opportunities for direct and/or indirect cross-transmission of pathogens. Comparatively few studies have investigated the epidemiology of gastro-intestinal nematode parasites, an ubiquitous and important community of parasites of ungulates, at the wildlife/livestock interface. In this study, we aimed to assess the influence of livestock proximity on the gastrointestinal nematode community of roe deer in a rural landscape located in southern France. Using ITS-2 rDNA nemabiome metabarcoding on fecal larvae, we analyzed the gastrointestinal nematode communities of roe deer and sheep. In addition, we investigated Haemonchus contortus nad4 mtDNA diversity to specifically test parasite circulation among domestic and wild host populations. The dominant gastrointestinal nematode species found in both the roe deer and sheep were generalist species commonly found in small ruminant livestock (e.g. H. contortus), whereas the more specialized wild cervid nematode species (e.g. Ostertagia leptospicularis) were only present at low frequencies. This is in marked contrast with previous studies that found the nemabiome of wild cervid populations to be dominated by cervid specialist nematode species. In addition, the lack of genetic structure of the nad4 mtDNA of H. contortus populations between host species suggests circulation of gastrointestinal nematodes between roe deer and sheep. We observed a seasonal variation in the nemabiome composition of roe deer. The risk of contact with livestock has a small influence on the nemabiome of roe deer. The parasite population of roe deer has been displaced by generalist livestock parasites because of many decades of sheep farming, not only for deer grazing close to pastures, but also at a larger regional scale. Overall, our results demonstrate significant exchange of gastrointestinal nematodes between domestic and wild ungulates with generalist species spilling over from domestic ungulates dominating wild cervid parasite communities.