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.畜牧业的发展以及欧洲野生有蹄类动物种群近期的扩张，为病原体直接或间接跨物种传播提供了有利条件。关于野生动物与家畜界面处胃肠道线虫寄生虫的流行病学的研究相对较少，而胃肠道线虫寄生虫是普遍且对有蹄类动物至关重要的寄生虫群体。在本研究中，我们旨在评估家畜邻近度对法国南部农村景观中鹿的胃肠道线虫群落的影响。通过ITS-2 rDNA线虫生物群组代谢组学分析粪便幼虫，我们研究了鹿和羊的胃肠道线虫群落。此外，我们还调查了 Haemonchus contortus nad4 线粒体DNA多样性，以特别测试寄生虫在家养和野生宿主种群间的循环。在鹿和羊中发现的占主导地位的胃肠道线虫物种为泛营养型物种，通常存在于小型反刍家畜中（例如 H. contortus），而更专业的野生鹿科动物线虫物种（例如 Ostertagia leptospicularis）仅以低频率存在。这与先前的研究形成鲜明对比，先前研究发现在野生鹿科动物群体的线虫生物群组中，鹿科动物专业线虫物种占主导地位。此外，H. contortus 线粒体DNA nad4 位点在宿主物种间的遗传结构缺乏，表明鹿和羊之间胃肠道线虫的循环。我们观察到鹿的线虫生物群组成存在季节性变化。与家畜接触的风险对鹿的线虫生物群有轻微影响。由于数十年的羊群养殖，鹿的寄生虫种群已被泛营养型家畜寄生虫所取代，这不仅是因为鹿在牧场附近的放牧，而且在更大区域尺度上也是如此。总体而言，我们的研究结果证明了家养和野生有蹄类动物之间胃肠道线虫的显著交换，泛营养型物种从家养有蹄类动物溢出，主导了野生鹿科动物寄生虫群落。