Strongylid nematodes in large terrestrial herbivores such as great apes, equids, elephants, and humans tend to occur in complex communities. However, identification of all species within strongylid communities using traditional methods based on coproscopy or single nematode amplification and sequencing is virtually impossible. High-throughput sequencing (HTS) technologies provide opportunities to generate large amounts of sequence data and enable analyses of samples containing a mixture of DNA from multiple species/genotypes. We designed and tested an HTS approach for strain-level identification of gastrointestinal strongylids using ITS-2 metabarcoding at the MiSeq Illumina platform in samples from two free-ranging non-human primate species inhabiting the same environment, but differing significantly in their host traits and ecology. Although we observed overlapping of particular haplotypes, overall the studied primate species differed in their strongylid nematode community composition. Using HTS, we revealed hidden diversity in the strongylid nematode communities in non-human primates, more than one haplotype was found in more than 90% of samples and coinfections of more than one putative species occurred in 80% of samples. In conclusion, the HTS approach on strongylid nematodes, preferably using fecal samples, represents a time and cost-efficient way of studying strongylid communities and provides a resolution superior to traditional approaches.

Central European Institute for Technology University of Veterinary and Pharmaceutical Sciences Brno Palackého tř 1946 1 612 42 Brno Czech Republic

Department of Infectious Disease Control Oita University School of Medicine 1 1 Idaigaoka Hasama Yufu Oita 879 5593 Japan

Department of Pathology and Parasitology Faculty of Veterinary Medicine University of Veterinary and Pharmaceutical Sciences Brno Palackého tř 1946 1 612 42 Brno Czech Republic

Department of Zoology Faculty of Science Charles University Viničná 7 Praha 128 44 Czech Republic

Fauna and Flora International Pembroke St Cambridge CB2 3QZ United Kingdom

The Czech Academy of Sciences Institute of Parasitology Branišovská 31 České Budějovice 370 05 Czech Republic

The Czech Academy of Sciences Institute of Vertebrate Biology Květná 8 Brno 603 65 Czech Republic

WWF CAR Bangui Central African Republic

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