BackgroundA novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first-time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments.MethodsA total of 158 fecal samples were collected (n=35 in 2007 and n=123 in 2013-2016) and cultured from

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... of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 x 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R.ResultsNematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1,008 sequences per sample. In total 16 operational taxonomical units (OTU), all had ≥98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which 10 are commonly associated with sheep. Multiple species were identified in all pre anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus.ConclusionsOur findings provide evidence that nemabiome analysis combined with diversity index analysis provide an objective methodology in the study of the efficacy of anthelmintic treatment, as both high and low abundant species were detected.