Irina Diekmann (Berlin / DE), Dr. Jürgen Krücken (Berlin / DE), Sandro Andreotti (Berlin / DE), Susann Mbedi (Berlin / DE), Tetiana Kuzmina (Kyiv / UA), CM Bredtmann (Berlin / DE), Heribert Hofer (Berlin / DE), Guillaume Sallé (Nouzilly / DE), Fernando Borges (Campo Grande / BR), MG de Freitas (Campo Grande / BR), JB Matthews (Penicuik / GB), TB Tzelos (Penicuik / GB), LMM de Carvalho (Lisboa / PT), MK Nielsen (Lexington, KY / US), S Sparmann (Berlin / DE), Prof. Dr. Georg von Samson-Himmelstjerna (Berlin / DE)
Abstract text
Introduction
Cyathostomins are ubiquitous in equids. While the nematode genera of equids have in general low species diversity, the Cyathostominae with 51 accepted species are the exception and represent a highly diverse multi-species complex. They are the most common parasites in the large intestine of equids and can cause severe clinical symptoms due to simultaneous excystation of the encysted larvae into the gut lumen. Anthelmintic resistance in parasitic nematodes is widespread and, therefore, of considerable veterinary and economic importance. Morphological identification and differentiation of these species requires detailed knowledge of their morphology and intensive training.
Objective
Improved tools for species identification are needed to investigate the interaction and influence of competing species within an ecological niche in horse intestine. The cytochrome c oxidase I (CO1) gene represents an efficient marker to estimate strongyle species richness. Compared to the internal transcribed spacer 2 (ITS-2) marker region, this marker region allows a reliable differentiation between Cylicostephanus calicatus and Coronocyclus coronatus.
Materials and methods
Therefore, the CO1 marker region was used to perform the Next Generation Sequencing (NGS) approach to detect strongyle population diversity. To compare the nemabiome between hosts with different geographical background and different treatment histories, an average of 10 treated and 10 untreated horses from Brazil, Ukraine, Kentucky, Scotland and Germany were examined and strongyle third stage larvae (L3) were obtained. Using Illumina MiSeq v300 amplicons were sequenced and a bioinformatic data processing pipeline was developed which provides a tool to distinguish between the different cyathostomin species.
Results
A total of 144 samples were analysed. On average, 38,500 reads could be generated per sample. Using the metabarcoding-dual-indexing approach, as well as bioinformatic pipelines, it was possible to assign the non-overlapping sequences to each individual sample and Strongylidae species could be detected.
Conclusions
Metabarcoding is a powerful tool which enables molecular characterization and investigation of the diversity and dynamics of strongyle populations within and between different hosts. The evaluation of the NGS data set allows identifying of the different cyathostomin species, per animal and the effects of geographic regions and management practices.