High species diversity of trichostrongyle parasite communities within and between Western Canadian commercial and conservation bison herds revealed by nemabiome metabarcoding

Abstract

BackgroundMany trichostrongylid nematode species are reported to infect bison, some of which are major causes of disase and production loss in North American bison herds. However, there is little information on the species distribution and relative abundance of these parasites in either commercial or conservation herds. This is largely because trichostrongylid nematode species cannot be distinguished by visual microscopic examination of eggs present in feces. Consequently, we have applied ITS2 rDNA nemabiome metabarcoding to describe the trichostrongyle parasite species diversity in 58 bison production groups derived from 38 commercial North American plains bison (Bison bison bison) herds from across western Canada, and two bison conservation herds located in Elk Island National Park (EINP) [plains bison and wood bison (Bison bison athabascae)] and one in Grasslands National Park (GNP) (plains bison).ResultsWe report much higher infection intensities and parasite species diversity in commercial bison herds than previously reported in beef cattle herds grazing similar latitudes. Predominant trichostrongyle parasite species in western Canadian commercial bison herds are those commonly associated with Canadian cattle, with Ostertagia ostertagi being the most abundant followed by Cooperia oncophora. Combined with high fecal egg counts in many herds, this is consistent with significant clinical and production-limiting gastrointestinal parasitism in western Canadian bison herds. However, Haemonchus placei was the most abundant species in five of the production groups. This is both surprising and important, as this highly pathogenic blood-feeding parasite has not been reported at such abundance, in any livestock species, at such northerly latitudes. The presence of Trichostrongylus axei as the most abundant parasite in four herds is also unusual, relative to cattle. There were striking differences in parasite communities between the EINP and commercial bison herds. Most notably, Orloffia bisonis was the predominant species in the wood bison herd despite being found at only low levels in all other herds surveyed.ConclusionsThis study represents the most comprehensive description of parasite communities in North American bison to date and illustrates the power of deep amplicon sequencing as a tool to study species diversity in gastrointestinal nematode communities.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2880-y) contains supplementary material, which is available to authorized users.

Assessing anthelmintic resistance risk in the post-genomic era: a proof-of-concept study assessing the potential for widespread benzimidazole-resistant gastrointestinal nematodes in North American cattle and bison

“…This provides the relative quantification of all nematode species present within mixedspecies samples. Exact details regarding the method and the original results can be found in Avramenko et al (2017) for the cattle samples from Canada, the USA and Brazil, while information pertaining to the Canadian bison samples can be found in Avramenko et al (2018). The nemabiome barcoding technique is fully described in Avramenko et al (2015) and at https:// www.nemabiome.ca/index.html, and the results from these previous papers have been included with permission.…”

Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

“…Still, it is unclear where to de ne the cut-off for discriminating between nematode species, as genetic isolation is generally used to de ne species boundaries rather than DNA differences [44]. Nevertheless, in agreement with previously studies on nemabiome in livestock and horses [16][17][18][19][20], a cut-off identity threshold of ≥99 seems reasonable. However, as shown in our study, the query cover also needs to be considered.…”

“…Recently the term "nemabiome" was created to describe the community structure of nematodes in ruminant livestock [16]. By using an Illumina based deep amplicon next generation pooled sequencing approach targeting the nematode ITS2 rRNA gene, a pipeline was developed which so far has been used to study the entire nemabiome in beef cattle [16], bison [17] and dairy cattle [18] in Canada and the US, as well as in UK sheep [19]. Similarly, the nemabiome of equines were recently studied by a slightly different methodology [20].…”

Sheep Nemabiome Diversity and Its Response to Anthelmintic Treatment in Swedish Sheep Herds

“…Still, it is unclear where to de ne the cut-off for discriminating between nematode species, as genetic isolation is generally used to de ne species boundaries rather than DNA differences [40]. Nevertheless, in agreement with previously studies on nemabiome in livestock and horses [16][17][18][19][20], a cut-off identity threshold of ≥ 99 seems reasonable. However, as shown in our study, the query cover also needs to be considered.…”

“…Like for any microbe NGS allows for the characterization of complex nematode communities and it open up new possibilities to identify community components even at low relative abundances at an unprecedented depth with minimal cost and labor. Recently the term "nemabiome" was created to describe the community structure of nematodes in ruminant livestock [16], By using an Illumina based deep amplicon next generation pooled sequencing approach targeting ITS-2 rDNA locus of the nematode rRNA genes, a pipeline was developed which so far has been used to study the entire nemabiome in beef cattle [16], bison [17] and dairy cattle [18] in Canada and the US, as well as in UK sheep [19]. Similarly, the nemabiome of equines were recently studied by a slightly different methodology [20].…”