Nemabiome of ibex and transhumant sheep

Wild and domestic ungulates can be infected with the same species of gastrointestinal parasitic nematodes. These parasitic nematodes have a free leaving stage in the environment that contributes to the ease of transmission of gastrointestinal nematodes at the interface of different host species. In addition, gastrointestinal nematodes have developed resistance to anthelmintics which is now considered a major problem for the livestock industry. In a context where wild and domestic ungulates share the same pastures, cross-transmission of resistant gastrointestinal nematodes between species could occur. In the Alps, domestic sheep are driven in the mountains each summer in areas where wild ungulates live. In particular, the Alpine ibex, Capra ibex is a protected mountain ungulate that is phylogenetically related to sheep and hosts nematode species common to sheep. In this study we investigated the nemabiome of sheep and ibex in three different areas of the French Alps to evaluate the parasites flow between the two host species. Our investigations are based on the metabarcoding of the ITS2 rDNA nemabiome using next generation sequencing. We also determined the frequency of anthelmintic-resistant nematodes in sheep and ibex to determine if ibex can host resistant strains. To that end, we sequenced the isotype 1 of the beta tubulin gene, in which mutations have been associated with benzimidazole resistance. We found that sheep and ibex have very similar nemabiomes before even this two species shared pasture and parasites, except for few nematode species, such as Marshallagia marshalli and Trichostrongylus axei. This suggests that the long-term co-occurrence of sheep and ibex on mountain pastures has promoted the exchange of gastrointestinal nematodes between sheep and ibex. The presence of sheep modified the nemabiome of ibex which may consequently cause a reduction of ibex fitness. Resistant nematodes were found on all sheep farms and in all Ibex populations, demonstrating that Ibex can host and shed resistant strains before transhumant sheep arrive on pastures. However, the relative contribution of ibex to nemabiome and the abundance of resistant nematodes in sheep remain to be determined.