The gastrointestinal nematodes of plains and Grevy's zebras: Phylogenetic relationships and host specificity

Abstract

Equids are chronically infected with parasitic strongyle nematodes. There is a rich literature on horse strongyles, but they are difficult to identify morphologically and genetic studies on strongyles infecting other equid species are few, hampering studies of host specificity. We sequenced expelled worms from two sympatric zebra species in central Kenya to expand the strongyle phylogeny and used DNA metabarcoding on faecal samples to genetically characterize zebra nemabiomes for the first time. We generated sequences for several species new to public genetic reference databases, all of which are typical strongyles in wild zebras (i.e., the three species of Cylindropharynx and Cyathostomum montgomeryi ), and identified their closest relatives. We also discovered an apparent fungus infecting a quarter of the expelled Crossocephalus viviparus worms, a hyperabundant nematode species in the family Atractidae, hinting at the possibility that zebra host-parasite dynamics may involve a zebra-fungus mutualism. The two zebra species had similar nemabiomes; we found a complete overlap in the list of nematode species they carry and very similar prevalence (i.e., proportion of hosts infected) for the different nematode species. Our study suggests limited host-specificity in zebra strongyles and high potential for transmission between the plains zebra and the endangered Grevy's zebra.

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

“…In addition to this higher resolutive power, the protein-coding nature of the COI barcode can be leveraged to denoise sequencing data ( Ramirez-Gonzalez et al, 2013 ). To date, metabarcoding experiments on strongylid species of equids have exclusively focused on the ITS-2 rDNA gene region, including community description in wild and domesticated equine populations ( Poissant et al, 2021 ; Sargison et al, 2022 ), the study of bioactive forage effect on cyathostomin species ( Malsa et al, 2022 ), the evaluation of drug efficacy in cyathostomin population ( Nielsen et al, 2022 ) or investigation of parasitic nematode community in plain zebras ( Tombak et al, 2021 ). This may owe to the existence of universal primers and the amplicon length that is a good fit for short-read sequencing platforms.…”

Large-herbivore nemabiomes: patterns of parasite diversity and sharing

“…Prevalence was assessed using qPCR on 550 fecal samples; community metrics were assessed on 281 of these samples that contained strongylid DNA. Samples were collected during six sampling bouts over five years (2013–2017), including a substantial subset of those analysed for plant and bacterial DNA in [43] and a set of zebra samples analysed in [35]. Samples were broadly dispersed and interspersed in space and time [43]; individual identities are unknown, but the spatio-temporal breadth and low ratio of sample sizes to species' abundances [44] means that duplicate samples from a given individual are highly unlikely.…”

“…We used the nemabiome database () [50] for taxonomic assignments. Inferences about diversity and network structure may be sensitive to the threshold used to cluster mOTUs; we present results from the 98% similarity threshold in the main text [35], but results were qualitatively similar using the 99% threshold (electronic supplementary material, Appendix II). We filtered the sample-by-mOTU table to account for any low-abundance reads in negative controls ( microDecon package [51]), dropped samples with fewer than 1000 reads, excluded mOTUs with less than 2% relative read abundance (RRA) per sample, and rarefied to 748 reads, the minimum number in any sample (validation of this approach is in electronic supplementary material, appendix I; see also [52]).…”

Effect of sainfoin (Onobrychis viciifolia) on cyathostomin eggs excretion, larval development, larval community structure and efficacy of ivermectin treatment in horses

“…However, it remains unclear whether the latter effects can be reproduced in vivo and if the putative effects of sainfoin extracts vary across various cyathostomin species. The recent development of an ITS-2-based metabarcoding approach has allowed the simultaneous identification and quantification of strongyle abundances in domestic horses (Mitchell et al ., 2019 ; Poissant et al ., 2021 ) or wild equids (Tombak et al ., 2021 ). This approach has been used to characterize the response to anthelmintic treatment of trichostrongylids in ruminants (Queiroz et al ., 2020 ; Halvarsson and Höglund, 2021 ) or the monitoring of drug resistance in these species (Queiroz et al ., 2020 ).…”